bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of Cobalt Oxide and Calcium‐Aluminum Oxide nano‐catalyst through Scanning Electron Microscopy, X‐ray diffraction, and Energy Dispersive X‐ray Spectroscopy
Authors: Gul Iram , Khan Shujaul Mulk , Mehmood Tariq , Ahmad Zeeshan , Badshah Hussain , Shah Hussain
Published: May 2020

The Cobalt Oxide and Calcium‐Aluminum Oxide nano‐catalysts were analyzed using Scanning Electronic Microscopy (SEM), X‐ray diffraction (XRD), and dispersive X‐ray spectroscopy (EDX) techniques. Preliminary results showed that the particles of Cobalt Oxide exhibit sponge like morphology and homogenous distribution as per confirmation via SEM. Its average particle size ranges to 30.6 nm demonstrating enormous number of pores and aggregative in nature. Its various peaks were ranging from 19.2 to 65.4 after XRD analysis. The highest intensity was observed at 36.9 position. The energy dispersive spectroscopy techniques were used to calculate the elements present in sample according to their weight and atomic percentage. The cobalt oxide contain cobalt as the most abundant element with 46.85 wt% and 18.01 atomic percent. It contain oxygen with 30.51 wt% and 43.19 atomic percent. Whereas, SEM of calcium aluminum oxide showed random morphology. According to the calculation of Scherrer equation regarding XRD analysis, it was distributed homogenously with particle size ranges from 30 to 40 nm. Its porous morphology was due to the interconnecting gaps between different particles. It result the eight peaks ranging from 18.1 to 62.7 in XRD spectrum. The highest intensity observed at 35.1 with average crystallite particle size of 25.6 nm. The calcium aluminum oxide contain aluminum 7.45 wt% and 6.93 atomic percent. The calcium was the most abundant element with54.7 wt% and 34.24 atomic percent followed by oxygen with 37.26 wt% and 58.42 atomic percent. It was concluded that the SEM, XRD, and EDX are the most significant techniques to characterize nano‐catalysts in particular and other compounds generally.
Surveillance strategy of Barrett's esophagus in the Asian region with particular reference to its locoregional epidemiology
Authors: Di Jia , Sharma Neel , Pérez Lady K M , Zhang Jun , Ho Khek‐Yu
Published: May 2020

Barrett's esophagus (BE) is a premalignant condition associated with the development of esophageal adenocarcinoma (EAC). Over the past decade, BE and its associated neoplasia has increased in prevalence globally. Current surveillance guidelines aimed to detect and treat BE‐associated dysplasia early in the hope of improving the morbidity and mortality of the condition. However, due to the lack of long‐term data and the proven benefit that surveillance actually improves mortality from EAC, the guidelines of the United States and Europe are slightly different. This review will focus on discussing the surveillance strategy for BE appropriate for the Asian region, taking into account the unique epidemiologic features of this disease in the Asian region.
Preparation of some novel thiazolidinones, imidazolinones, and azetidinone bearing pyridine and pyrimidine moieties with antimicrobial activity
Authors: Bakr Rania B. , Elkanzi Nadia A. A.
Published: May 2020

By aiming to design new antimicrobial agents, we prepared new series of thiazolidin‐4‐ones(12a–d), imidazolin‐4‐ones(13a–d), and azetidin‐2‐ones (14a–d), having pyridine and pyrimidine moieties. Chemical structures of these derivatives were elucidated by the use of spectral and elemental analyses. All the new substituted pyridopyrimidines were subjected to in vitro antimicrobial testing by estimating the zone of inhibition toward Bacillus subtilis and Staphylococcus aureus, as examples of bacterial species, in addition to Aspergillus flavus and Candida albicans, as examples of fungal species. The results of antimicrobial testing detected that all the screened derivatives displayed antibacterial effect; especially azetidin‐2‐one derivative, (14c), was the most active one. Regarding the antifungal potential, only thiazolidinone derivatives, 12a and 12c, and the imidazolinone, 13c, displayed inhibitory activity toward Aspergillus flavus, while all the tested compounds, 12a–d, 13a–d, and 14a–d, except 14a, produced inhibitory potential toward Candida albicans. Docking studies of the most active antimicrobial agents, 12c, 13c, and 14c, within GLN‐6‐P, recorded good scores with several binding interactions with the active site.
Mutations in GET4 disrupt the transmembrane domain recognition complex pathway
Authors: Tambe Mitali A. , Ng Bobby G. , Shimada Shino , Wolfe Lynne A. , Adams David R. ,   Undiagnosed Diseases Network, Gahl William A. , Bamshad Michael J. , Nickerson Deborah A. , Malicdan May C. V. , Freeze Hudson H.
Published: May 2020

The transmembrane domain recognition complex (TRC) targets cytoplasmic C‐terminal tail‐anchored (TA) proteins to their respective membranes in the endoplasmic reticulum (ER), Golgi, and mitochondria. It is composed of three proteins, GET4, BAG6, and GET5. We identified an individual with compound heterozygous missense variants (p.Arg122His, p.Ile279Met) in GET4 that reduced all three TRC proteins by 70% to 90% in his fibroblasts, suggesting a possible defect in TA protein targeting. He presented with global developmental delay, intellectual disabilities, seizures, facial dysmorphism, and delayed bone age. We found the TA protein, syntaxin 5, is poorly targeted to Golgi membranes compared to normal controls. Since GET4 regulates ER to Golgi transport, we hypothesized that such transport would be disrupted in his fibroblasts, and discovered that retrograde (but not anterograde) transport was significantly reduced. Despite reduction in the three TRC proteins, their mRNA levels were unchanged, suggesting increased degradation in patient fibroblasts. Treating fibroblasts with the FDA‐approved proteasome inhibitor, bortezomib (10 nM), restored syntaxin 5 localization and nearly normalized the levels of all three TRC proteins. Our study identifies the first individual with GET4 mutations.
Stereotypical behavioural cues — but not their order — influence credibility judgements
Authors: Bogaard Glynis , Meijer Ewout H.
Published: May 2020

To what extent stereotypical deceptive behaviours such as gaze aversion and fidgeting actually influence people's credibility judgements remain largely unknown. In this study, we directly manipulated the presence/absence of such behaviours to investigate this. Participants were shown four truthful videos in which we manipulated the presence of stereotypical cues and asked them to judge how credible the person in each video is. Moreover, research consistently shows that decision making is influenced by various cognitive biases. One example is the primacy effect, which implies that people form an opinion early in the decision process. Information acquired early will have the largest influence on how subsequent information will be interpreted. To investigate a possible primacy effect, we also manipulated whether these cues were present towards the beginning or the end of the video (i.e. the timing of the manipulation). In line with our expectations, the presence of stereotypical cues significantly lowered the observed credibility, showing that the presence of these cues indeed influences credibility judgements. The timing of the cues had no effect.
The impact of laryngopharyngeal reflux disease on 95 hospitalized patients with COVID‐19 in Wuhan, China: A retrospective study
Authors: Jiang Guiyuan , Cai Yanping , Yi Xue , Li Yanping , Lin Yong , Li Qing , Xu Jingqing , Ke Mingyao , Xue Keying
Published: May 2020

Studies have demonstrated that comorbidities, especially cardiovascular and endocrine diseases, correlated with poorer clinical outcomes. However, the impact of digestive system diseases has not been issued. The aim of this study is to determine the impact of laryngopharyngeal reflux disease (LPRD) on hospitalized patients with coronavirus disease 2019 (COVID‐19). We extracted clinical data regarding 95 patients in Wuhan Jinyintan Hospital, Wuhan, China, between 26 January and 21 February 2020. The Reflux Symptom Index (RSI) was used to assess the presence and severity of LPRD. An RSI  greater than  13 is considered to be abnormal. A total of 95 patients with COVID‐19 were enrolled, with 61.1% (58/95), 32.6% (31/95), and 6.3% (6/95) being moderately ill, severely ill, and critically ill, respectively. In this study, 38.9% (37/95) of the patient had an RSI score over 13, which was indicative of LPRD. In univariable analysis, the age and RSI scores of severely or critically ill patients were statistically significantly higher than patients with moderate disease (P  =  .026 and P = .005, respectively). After controlling for age difference in a multivariable model, the RSI greater than 13, compared to RSI equal to  0, was associated with significantly higher risk of severe infection (P < .001; odds ratio [OR] = 11.411; 95% confidence interval [CI], 2.95‐42.09) and critical infection (P = .028; OR= 19.61; 95% CI, 1.38‐277.99). Among hospitalized patients with COVID‐19, RSI scores greater than 13, indicative of LPRD, correlated with poorer clinical outcomes. The prevalence of LPRD may be higher than the general population, which indicated that COVID‐19 can impair the upper esophageal sphincter and aggravate reflux.
miRNA‐21 deficiency impairs alveolar socket healing in mice
Authors: Strauss Franz Josef , Stähli Alexandra , Kobatake Reiko , Tangl Stefan , Heimel Patrick , Apaza Alccayhuaman Karol Alí , Schosserer Markus , Hackl Matthias , Grillari Johannes , Gruber Reinhard
Published: May 2020

Background

MicroRNAs (miRNAs) are small noncoding RNAs demonstrated as critical post‐transcriptional modulators in dental tissues and bone regeneration, particularly miR‐21‐5p. However, the role of miR‐21‐5p in the healing of alveolar sockets following tooth extraction remains unknown. In this study we evaluated the influence of miR‐21‐5p in the healing of alveolar socket after tooth extraction.

Methods

Eight miR‐21‐5p knockout mice and eight littermate controls underwent tooth extraction of the upper right incisor. After a healing period of 14 days microCT and histological analyses were performed.

Results

MicroCT analysis showed that the percentage of bone in the extraction socket was significantly higher in the control group than in the miR‐21 knockout mice; either in the coronal (39.0%, CI 31.8 to 48.0 versus 23.0%, CI 17.8 to 35.2, P = 0.03) or in the middle part of the alveolar socket (56.0%, CI 50.9 to 62.5 versus 43.5% CI 28.6 to 54.6, P = 0.03). These differences were not noted in the apical part of the extraction socket. Histological analysis supported the microCT findings. Newly bone volume per tissue volume (BV/TV) was significantly higher in the control group when compared to miR‐21 knockout mice, 27.4% (CI 20.6 to 32.9) versus 19.0% (CI 14.7 to 21.5, P < 0.05), respectively. Surprisingly, no evident signs of buccal bone resorption were observed in both groups.

Conclusion

Despite the limitation of one observation period, these findings suggest that miR‐21‐5p delays the early healing of alveolar socket following tooth extraction. Whether miR‐21‐5p is essential for healing of alveolar sockets remains to be elucidated.
Quantitative determination of trace phenazopyridine in human urine samples by hyphenation of dispersive solid‐phase extraction and liquid‐phase microextraction followed by gas chromatography/mass spectrometry analysis
Authors: Seidi Shahram , Mohammadi Fahimeh , Tajik Mohammad , Baharfar Mahroo , Mohammadi Abdorreza , Otoufat Tohid
Published: May 2020

Magnetic dispersive solid‐phase extraction followed by dispersive liquid−liquid microextraction coupled with gas chromatography/mass spectrometry was applied for the quantitative analysis of phenazopyridine in urinary samples. Magnetic dispersive solid‐phase extraction was carried out using magnetic graphene oxide nanoparticles modified by poly(thiophene‐pyrrole) copolymer. The eluting solvent of this step was used as the disperser solvent for the dispersive liquid−liquid microextraction procedure. To reach the maximum efficiency of the method, effective parameters including sorbent amount, adsorption time, type and volume of disperser and extraction solvents, pH of the sample solution, and ionic strength as well as desorption time, and approach were optimized, separately. Characterization of the synthesized sorbent was studied by utilizing infrared spectroscopy, scanning electron microscopy, and energy‐dispersive X‐ray analysis. Calibration curve was linear in the range of 0.5−250 ng/mL (R2 = 0.9988) with limits of detection and quantification of 0.1 and 0.5 ng/mL, respectively. Intra‐ and interday precisions (RSD%, n = 3) of the method were in the range of 4.6−5.4% and 4.0−5.5%, respectively, at three different concentration levels. Under the optimal condition, this method was successfully applied for the determination of phenazopyridine in human urine samples. The relative recoveries were obtained in the range of 85.0−89.0%.
Filling of Fine and Core Biopsy Needles With the Contrast Agent Sulfur Hexafluoride
Authors: Thunswärd Per , Nilsson Anders , Ahlström Håkan
Published: May 2020

Objectives

To investigate whether the ex vivo and in vitro ultrasound visibility of fine needles (FNs) and core biopsy needles (CNBs) can be improved by filling them with an ultrasound contrast agent.

Methods

After needle filling with the contrast agent sulfur hexafluoride, punctures with FNs and CBNs were recorded in the B‐mode and contrast‐specific imaging mode (10 observations in each of the 4 groups). Recordings were made in both butchered bovine liver (experiment I) and a water bath (experiment II). Air and normal saline were used as controls (total n = 120 for each experiment). In experiment I, 4 ultrasound specialists subjectively assessed the relative needle visibility in the recordings by using an arbitrary scale (integers 0–10). In experiment II, the contrast‐to‐noise ratio was calculated for both the entire needle course and the needle tip area.

Results

In experiment I, subjective visibility was increased compared with both controls only for CBNs in the contrast‐specific imaging mode (P < .01). In experiment II, the contrast‐to‐noise ratio for both the entire needle course and the needle tip area increased compared with both controls for both FNs and CBNs in the contrast‐specific imaging mode (P < .05).

Conclusions

Ultrasound contrast agent needle filling is a promising new method to increase the visibility of CBNs in the contrast‐specific imaging mode. This finding needs to be confirmed in vivo before its clinical value can be assessed.
Focused Cardiac Ultrasound in Dyspnea of Unclear Etiology in the Emergency Department
Authors: Balderston Jessica R. , Sternberg Michael E. , Joyce J. Michael , Evans David P. , Gertz Zachary M.
Published: May 2020

Objectives

We evaluated the utility of focused cardiac ultrasound to predict the length of stay in patients presenting to the emergency department with dyspnea of unclear etiology.

Methods

Patients with focused cardiac ultrasound examinations performed in the emergency department for dyspnea over a 34‐month period were retrospectively identified. Patients were excluded if they had a prior diagnosis of heart failure, dialysis requirement, or an etiology of dyspnea unrelated to the volume status. Left ventricular function was categorized as normal or reduced, and the inferior vena cava was categorized as normal or increased volume. A fast limited ultrasound to investigate dyspnea (FLUID) score was calculated by adding 1 point for reduced left ventricular function and 1 point for increased volume, producing a score of 0, 1, or 2.

Results

There were 123 patients included. There was a significant correlation between the FLUID score and length of stay, with longer stays for higher scores (FLUID score 0, 7.4 hours median; FLUID score 1, 2.34 days; FLUID score 2, 5.56 days; analysis of variance P < .001). Of the other variables collected, only age, hypertension, diabetes, heart rate, and brain natriuretic peptide were significantly correlated with the length of stay. A multivariate analysis including those variables and the FLUID score showed that the FLUID score was the strongest independent predictor of the length of stay.

Conclusions

Focused cardiac ultrasound and calculation of a FLUID score for patients with undifferentiated dyspnea can be a powerful tool to predict the hospital length of stay.
Association of CARD8 Activating Polymorphism With Bone Erosion in Cholesteatoma Patients
Authors: Sangal Neel , Yan John , Pryor Jessica , Elias Marcus L. , Joseph Biju , Ulloa Luis , Jyung Robert W.
Published: May 2020

Objectives

We compared the incidence of polymorphisms activating the NLRP3 inflammasome between controls and patients with cholesteatoma and its potential association with bone erosion in patients with cholesteatoma.

Methods

This is a case‐control study assessing the mutation rates in genes of interest in patients with and without cholesteatoma. A total of 133 saliva samples from control (n = 65) and cholesteatoma (n = 68) patients were collected for DNA extraction. Caspase recruitment domain family member 8 (CARD8) (AA: homozygous wild type, AT: heterozygous, TT: homozygous mutant polymorphism) and NLRP3 (CC: homozygous wild type, CA: heterozygous, AA: homozygous mutant) polymorphisms were analyzed with TaqMan single‐nucleotide polymorphism (SNP) quantitative polymerase chain reaction (ThermoFisher Scientific, Waltham, MA). Mutation status was correlated with a novel bone erosion scoring model developed as a part of this study. Summary statistics, including frequencies (%) and median (Q1, Q3) were used to describe the sample.

Results

The presence of CARD8 and NLRP3 homozygous wild‐type polymorphisms were generally similar for the control and cholesteatoma patient groups. CARD8 homozygous TT polymorphisms were an exception, occurring more frequently in patients who developed a cholesteatoma compared to the control group (29% vs. 10%, P = .009). Those patients with CARD8 homozygous TT polymorphism had higher median scores of bone erosion as compared to subjects with nonhomozygous mutant genotypes (median [interquartile range]: 4.0 [3.0, 5.5] vs. 2.5 [1.0, 3.5], P = .0142).

Conclusion

Cholesteatoma patients have a significant, twofold higher incidence of CARD8 homozygous TT polymorphism. Furthermore, cholesteatoma patients with this homozygous polymorphism had greater bone erosion rates than controls. These findings suggest that genetic mutations may increase host susceptibility to cholesteatomas. Specifically, the CARD8 TT polymorphism may influence the severity of cholesteatoma‐induced bone erosion.

Level of Evidence: 3b
Left Hepatic Vein Preferential Approach Based on Anatomy Is Safe and Feasible for Laparoscopic Living Donor Left Lateral Sectionectomy
Authors: Lu Lu , Wang Zheng‐Xin , Zhu Wen‐Wei , Shen Cong‐Huan , Tao Yi‐Feng , Ma Zhen‐Yu , Zhang Quan‐Bao , Li Rui‐Dong , Jia Hu‐Liang , Qin Lun‐Xiu , Chen Jin‐Hong
Published: May 2020

We assess the safety and feasibility of the left hepatic vein preferential approach (LHVPA) based on left hepatic vein (LHV) anatomy for living donor laparoscopic left lateral sectionectomy (LLLS). Data from 50 donors who underwent LLLS in Huashan Hospital from October 2016 to November 2019 were analyzed retrospectively. On the basis of the classification of the LHV anatomy, the vein was defined as the direct import type, upper branch type, or indirect import type. A subgroup analysis was performed to compare the outcomes between the LHVPA and non‐LHVPA groups. All 50 patients underwent pure LLLS. The mean operative duration was 157.5 ± 29.7 minutes. The intraoperative blood loss was 160.4 ± 97.5 mL. No complications more severe than grade 3 occurred. LHVPA was applied in 13 patients, whereas non‐LHVPA was applied in 10 patients with the direct import type and upper branch type anatomy. The operative duration was shorter in the LHVPA group than the non‐LHVPA group (142.7 ± 22.0 versus 173.0 ± 22.8 minutes; P = 0.01). Intraoperative blood loss was reduced in the LHVPA group compared with the non‐LHVPA group (116.2 ± 45.6 versus 170.0 ± 63.3 mL; P = 0.02). The length of the LHV reserved extrahepatically in the LHVPA group was longer than in the non‐LHVPA group (4.3 ± 0.2 versus 3.3 ± 0.3 mm; P = 0.01). Fewer reconstructions of the LHV in the direct import type anatomy were required for the LHVPA group than for the non‐LHVPA group (0/8 versus 4/6). LHVPA based on the LHV anatomy is recommended in LLLS because it can further increase the safety and the efficiency of surgery for suitable donors.
The optimization system for preparation of TG1 competent cells and electrotransformation
Authors: Chai Dafei , Wang Gang , Fang Lin , Li Huizhong , Liu Shanshan , Zhu Haiying , Zheng Junnian
Published: May 2020

An efficient electrotransformation system that includes electrocompetent cells is a critical component for the success of large‐scale gene transduction and replication. The conditions of TG1 competent cell preparation and optimal electrotransformation were evaluated by investigating different parameters. Certain parameters for preparation of TG1 competent cells (≥8 × 1010 colony forming units (cfu)/μg DNA) include optimum culture time of monoclonal bacteria (8–10 hr), amplification growth concentration (approximately OD600 = 0.45), and culture volume (400 ml in 2 L conical flask). With increased storage of competent cells at −80°C, electrotransformation efficiency gradually decreased, but it remains greater than ≥ 1010 cfu/μg DNA 3 months later. Moreover, the recovery time of electrotransformation also influenced electrotransformation efficiency (1.5–2 hr for optimization). The optimized transformation efficiency of TG1 (≥8 × 1010 cfu/μg DNA) was observed under suitable electric voltage (2.5 kV), electric intensity (15 kV/cm), and electric time (3.5 ms) of electricity for plasmid transformation. Optimized DNA amount (0.01–100 ng) dissolved in water led to the high efficiency of plasmid transformation (≥8 × 1010 cfu/μg DNA), but had low efficiency when dissolved in T4 ligation buffer (≤3 × 1010 cfu/μg DNA). These results indicated that an optimized TG1 transformation system is useful for high electrotransformation efficiency under general laboratory conditions. The optimized TG1 transformation system might facilitate large‐scale gene transduction for phage display library construction.
Functional Motor Disorders Mimicking Symptoms Upon Resolution of Cerebrovascular Disease
Authors: Paio Fabio , Antelmi Elena , Conti Enrico , Di Vico Ilaria , Tinazzi Michele
Published: May 2020

Background

Functional motor disorders encompass a variety of manifestations characterized by abnormal movements that are clinically incongruent with those known to be caused by neurological diseases.

Cases

We report 2 cases in which functional motor disorders developed after complete recovery of motor symptoms originating from underlying vascular brain lesions. The first case describes a young woman who developed a motor and sensory hemisyndrome after surgical removal of a postrolandic cavernoma. The second describes a 16‐year‐old girl who presented with a mixed component tremor after ventricular derivation and endovascular embolization for rupture of a brainstem arteriovenous malformation.

Conclusion

Motor symptoms and signs attributed to an underlying lesion may trigger “pure” functional motor disorders. In such cases, the differential diagnosis may be even more challenging. However, diagnosis of a functional rather than a defined structural disorder can be achieved by a “positive diagnostic process,” considering the findings of internal inconsistency and incongruity.
Magnetic Resonance Imaging Biomarkers Distinguish Normal Pressure Hydrocephalus From Progressive Supranuclear Palsy
Authors: Quattrone Andrea , Sarica Alessia , La Torre Domenico , Morelli Maurizio , Vescio Basilio , Nigro Salvatore , Barbagallo Gaetano , Nisticò Rita , Salsone Maria , Arcuri Pier Paolo , Novellino Fabiana , Bianco Maria Giovanna , Arabia Gennarina , Cascini Giuseppe , Quattrone Aldo
Published: May 2020

Background

Idiopathic normal pressure hydrocephalus and PSP share several clinical and radiological features, making differential diagnosis, at times, challenging.

Objectives

To differentiate idiopathic normal pressure hydrocephalus from PSP using MR volumetric and linear measurements.

Methods

Twenty‐seven idiopathic normal pressure hydrocephalus patients, 103 probable PSP patients, and 43 control subjects were consecutively enrolled. Automated ventricular volumetry was performed using Freesurfer 6 on MR T1‐weighted images. Linear measurements, such as callosal angle and a new measure, termed MR Hydrocephalic Index, were calculated on MR T1‐weighted images. Receiver operating characteristic analyses were used for differentiating between patient groups. Generalizability and reproducibility of the results were validated, dividing each participant group in two cohorts used as training and testing subsets.

Results

Ventricular volumes and linear measurements (callosal angle and Magnetic Resonance Hydrocephalic Index) revealed greater ventricular enlargement in patients with idiopathic normal pressure hydrocephalus than in PSP patients and controls. PSP patients had ventricular volume larger than controls. Automated ventricular volumetry and Magnetic Resonance Hydrocephalic Index were the most accurate measures (98.5%) in differentiating patients with idiopathic normal pressure hydrocephalus from PSP patients, whereas callosal angle misclassified several PSP patients and showed low positive predictive value (70.0%) in differentiating between these two diseases. All measurements accurately differentiated idiopathic normal pressure hydrocephalus patients from controls. Accuracy values obtained in the training set (automated ventricular volumetry, 98.4%; Magnetic Resonance Hydrocephalic Index, 98.4%; callosal angle, 87.5%) were confirmed in the testing set.

Conclusions

Our study demonstrates that AVV and Magnetic Resonance Hydrocephalic Index were the most accurate measures for differentiation between idiopathic normal pressure hydrocephalus and PSP patients. Magnetic Resonance Hydrocephalic Index is easy to measure and can be used in clinical practice to prevent misdiagnosis and ineffective shunt procedures in idiopathic normal pressure hydrocephalus mimics. © 2020 International Parkinson and Movement Disorder Society
A novel prognostic model based on multi‐omics features predicts the prognosis of colon cancer patients
Authors: Yang Haojie , Jin Wei , Liu Hua , Wang Xiaoxue , Wu Jiong , Gan Dan , Cui Can , Han Yilin , Han Changpeng , Wang Zhenyi
Published: May 2020

Background

As a common malignant tumor in the colon, colon cancer (CC) has high incidence and recurrence rates. This study is designed to build a prognostic model for CC.

Methods

The gene expression dataset, microRNA‐seq dataset, copy number variation (CNV) dataset, DNA methylation dataset, and transcription factor (TF) dataset of CC were downloaded from UCSC Xena database. Using limma package, the differentially methylated genes (DMGs), and differentially expressed genes (DEGs) and miRNAs (DEMs) were identified. Based on random forest method, prognostic model for each omics dataset were constructed. After the omics features related to prognosis were selected using logrank test, the prognostic model based on multi‐omics features was built. Finally, the clinical phenotypes correlated with prognosis were screened using Kaplan–Meier survival analysis, and the nomogram model was established.

Results

There were 1625 DEGs, 268 DEMs, and 386 DMGs between the tumor and normal samples. A total of 105, 29, 159, five, and six genes/sites significantly correlated with prognosis were identified in the gene expression dataset (GABRD), miRNA‐seq dataset (miR‐1271), CNV dataset (RN7SKP247), DNA methylation dataset (cg09170112 methylation site [located in SFSWAP]), and TF dataset (SIX5), respectively. The prognostic model based on multi‐omics features was more effective than those based on single omics dataset. The number of lymph nodes, pathologic_M stage, and pathologic_T stage were the clinical phenotypes correlated with prognosis, based on which the nomogram model was constructed.

Conclusion

The prognostic model based on multi‐omics features and the nomogram model might be valuable for the prognostic prediction of CC.
Roles of HOTAIR in lung cancer susceptibility and prognosis
Authors: Ren Meng‐Meng , Xu Sen , Wei Yu‐Bo , Yang Juan‐Juan , Yang Ya‐Nan , Sun Shan‐Shan , Li You‐Jie , Wang Ping‐Yu , Xie Shu‐Yang
Published: May 2020

Background

Long noncoding (lncRNA) single‐nucleotide polymorphisms (SNPs) are associated with the susceptibility to the development of various malignant tumors. The aim of this study was to investigate the roles of HOX transcript antisense intergenic RNA (HOTAIR) and its SNPs in lung cancer.

Methods

Initially, the expression of HOTAIR in different tumors was investigated using the online Gene Expression Profiling Interactive Analysis (GEPIA) resource. Three SNPs (rs920778, rs1899663, and rs4759314) of HOTAIR were identified using the MassArray system. Following this, the relationship between these SNPs and susceptibility to lung cancer was investigated.

Results

Expression of HOTAIR was found to increase in a variety of cancers, including nonsmall cell lung cancer (NSCLC). We found that the genotypes of these SNPs (rs920778, rs1899663, and rs4759314) were not significantly associated with lung cancer type, family history, lymph node metastasis, or lung cancer stage. In gender stratification, the results of rs920778 genotypes showed that, compared to genotype AA, the AG (OR = 0.344, 95% CI: 0.133–0.893, p = .028) and AG + GG (OR = 0.378, 95% CI: 0.153–0.932, p = .035) genotypes of rs920778 are protective factors against NSCLC in females. In smoking stratification, compared with AA of rs920778, the genotype AG + GG (OR = 0.507, 95% CI: 0.263–0.975, p = .042) was a protective factor against NSCLC in nonsmoking people. No statistical differences were observed in the classifications of rs1899663 and rs4759314 genotypes. Linkage disequilibrium analysis revealed a high linkage disequilibrium between the rs920778 and rs1899663 (D′ = 0.99, r2 = .74), rs920778 and rs4759314 (D′ = 0.85, r2 = .13), and rs1899663 and rs4759314 (D′ = 0.79, r2 = .00).

Conclusion

Our study demonstrated that HOTAIR expression increased in NSCLC, and that the genotypes of rs920778 could be useful in the diagnosis and prognosis of lung cancer.
Magnetohydrodynamic convection behaviours of nanofluids in non‐square enclosures: A comprehensive review
Authors: Giwa Solomon Olanrewaju , Sharifpur Mohsen , Ahmadi Mohammad Hossein , Meyer Josua Petrus
Published: May 2020

Nanofluid is a special thermal transport medium that has recently received unprecedented attention due to its improved heat transfer performance compared with conventional fluids. Numerous researches have been conducted on the natural convection characteristics of different nanofluids in various configurations of cavities due to the enormous applications of natural convection in environmental, petrochemical, medical, aviation and space technology, industrial, and many more areas. This paper presented a comprehensive review on the influence of different types, magnitudes, and orientations of magnetic field on the hydrodynamic natural convection heat and flow characteristics of diverse nanofluids in specialised non‐square enclosures, which was lacking in the public domain. The emergence of a magnetic field as a tool for the manipulation of convective flow and heat transfer behaviours of nanofluids in non‐square enclosures has been extensively reviewed. The influence of several variables such as controlling parameters, heat distribution methods, thermal and concentration boundary conditions, magnetic field types, numerical methods, correlation types, nanofluid types, heaters types, numbers and length, and slip conditions, on the magnetohydrodynamic (MHD) natural convection flow and heat transfer behaviours of nanofluid in non‐square cavities was brought to the spotlight for discussion. The concepts of bioconvection, micro‐polar nanofluid, bio‐nanofluid (green nanofluid), ionic nanofluid, and hybrid nanofluid were also discussed for the first time in relation to natural convection. Special cases of MHD natural convection in non‐square cavities involving hybrid nanofluids and micro‐polar nanofluids were also presented herein. The application of several numerical methods (which was the major approach studied so far) to investigate the hydromagnetic behaviours of nanofluids in non‐square cavities was the focus of this work.
Comparison of robust to standardized CT radiomics models to predict overall survival for non‐small cell lung cancer patients
Authors: Vuong Diem , Bogowicz Marta , Denzler Sarah , Oliveira Carol , Foerster Robert , Amstutz Florian , Gabryś Hubert S. , Unkelbach Jan , Hillinger Sven , Thierstein Sandra , Xyrafas Alexandros , Peters Solange , Pless Miklos , Guckenberger Matthias , Tanadini‐Lang Stephanie
Published: May 2020

Background

Radiomics is a promising tool for the identification of new prognostic biomarkers. Radiomic features can be affected by different scanning protocols, often present in retrospective and prospective clinical data. We compared a computed tomography (CT) radiomics model based on a large but highly heterogeneous multicentric image dataset with robust feature pre‐selection to a model based on a smaller but standardized image dataset without pre‐selection.

Materials and methods

Primary tumor radiomics was extracted from pre‐treatment CTs of IIIA/N2/IIIB NSCLC patients from a prospective Swiss multicentric randomized trial (npatient = 124, ninstitution = 14, SAKK 16/00) and a validation dataset (npatient = 31, ninstitution = 1). Four robustness studies investigating inter‐observer delineation variation, motion, convolution kernel, and contrast were conducted to identify robust features using an intraclass correlation coefficient threshold >0.9. Two 12‐months overall survival (OS) logistic regression models were trained: (a) on the entire multicentric heterogeneous dataset but with robust feature pre‐selection (MCR) and (b) on a smaller standardized subset using all features (STD). Both models were validated on the validation dataset acquired with similar reconstruction parameters as the STD dataset. The model performances were compared using the DeLong test.

Results

In total, 113 stable features were identified (nshape = 8, nintensity = 0, ntexture = 7, nwavelet = 98). The convolution kernel had the strongest influence on the feature robustness (<20% stable features). The final models of MCR and STD consisted of one and two features respectively. Both features of the STD model were identified as non‐robust. MCR did not show performance significantly different from STD on the validation cohort (AUC [95%CI] = 0.72 [0.48–0.95] and 0.79 [0.63–0.95], p = 0.59).

Conclusion

Prognostic OS CT radiomics model for NSCLC based on a heterogeneous multicentric imaging dataset with robust feature pre‐selection performed equally well as a model on a standardized dataset.
Otolith and Scale-Based Growth Standards for Lotic Smallmouth Bass
Authors: Starks Trevor A. , Rodger Anthony W.
Published: May 2020

Comparisons of local population growth rates to species averages are valuable for natural resource managers because growth rates provide an integrated evaluation of abiotic and biotic factors that regulate growth in a fishery and may inform management decisions. Thus, species-specific standard growth models pave the way for fisheries scientists to efficiently complete comparisons, evaluate status, and determine the potential of a fishery for meeting goals and objectives. Growth standards have been published for numerous freshwater fishes; however, growth standards commonly neglect differences among populations of the same species that reside in different habitat types (e.g., lotic versus lentic habitats). Furthermore, studies may use data sets that are based on age estimates from various aging structures, even those with known biases, when creating standard growth models. Our study developed a standard growth model for lotic-dwelling Smallmouth Bass Micropterus dolomieu based on over 11,000 fish across their range in the United States. Due to differences in parameter estimates between standard growth equations that are generated with otolith- and scale-aged fish, separate standard growth models were created for each structure. Standard growth models were used to calculate the following growth standards: predicted age-specific standard length, percentile distributions of age-specific standard length, and estimates of the time required to reach specified size-classes for each aging structure. Thus, standard growth models and growth standards are presented for the two most common aging structures, which will facilitate comparisons of lotic Smallmouth Bass populations by providing equitable growth equations regardless of the aging structure that is used by researchers.
Exploring residential care aide experiences with oral malodour in long‐term care
Authors: Dhami Charanpreet Singh , Donnelly Leeann R.
Published: May 2020

Aim

To determine what experiences do residential care aides (RCAs) have with individuals living with oral malodour in a long‐term care (LTC) facility?

Design

Study investigation was done using an interpretive qualitative approach paired with a social constructivism interpretive framework.

Methods

The study was conducted in May of 2015 through face‐to‐face interviews with RCAs, which were recorded and transcribed verbatim, observations of RCAs in their work environment, as well as RCA personal logs of their daily experiences with odour during caregiving. Thereafter, data were analysed and coded for emerging themes.

Results

Five major themes were identified after grouping the codes: 1) attitudes and behaviours when caring for residents with malodour; 2)RCA knowledge of oral malodour; 3) level of job satisfaction among RCAs that care for residents with malodour; 4) culture and malodour; and 5) challenges of care giving compounded by malodour. These themes depict the overall experiences of study participants.
Registration of 11 diverse sorghum germplasm lines for grain and silage hybrid production
Authors: Horne David W. , Patil Nikhil Y. , Klein Robert R. , Miller Fred R. , Hoffmann Leo , Klein Patricia E. , Rooney William L.
Published: May 2020

Genotypic variance is necessary for trait improvement because limited diversity can reduce genetic gains in crop improvement. To maintain genetic diversity, a wealth of germplasm exists in the USDA‐ARS sorghum [Sorghum bicolor (L.) Moench] collection, but most of the accessions are not adapted to temperate climates. To address this issue, the Reinstated Sorghum Conversion program (RSC, ∼2009–2014) converted 155 tropical accessions to combine height and early maturing F3 and BC1F3 families. Here, 11 germplasm lines Tx3429 to Tx3439 (Reg. no. GP‐889, PI 692640 to Reg. no. GP‐899, PI 692650) released by Texas A&M AgriLife Research in 2019 and derived from the RSC program are described. This germplasm was derived from F3, BC1F3, and BC1F4 RSC families that were selected based on testcross hybrid performance for either grain or silage production. Six lines are grain sorghum pollinators, one line is a seed parent, and four lines are silage pollinators. These lines combined agronomic productivity with greater genetic diversity as confirmed via genotyping‐by‐sequencing. These 11 parental germplasms are being released to provide new genetic diversity for forage and grain hybrid improvement programs.
FIELDimageR: An R package to analyze orthomosaic images from agricultural field trials
Authors: Matias Filipe Inácio , Caraza‐Harter Maria V. , Endelman Jeffrey B.
Published: May 2020

Remote sensing is revolutionizing the phenotyping of agricultural field trials, but for many researchers, the extraction of plot‐level results is a bottleneck. We have developed the R package FIELDimageR as a user‐friendly tool to analyze orthomosaic images containing many plots. The basic workflow involves cropping and rotating the image, followed by the creation of a shapefile based on the experimental design. The package includes functions to calculate the number of plants per plot, canopy cover percentage, vegetation indices, and plant height. FIELDimageR is publicly available as a GitHub repository (https://github.com/filipematias23/FIELDimageR).
Ultrasound assessment of diaphragmatic function in type 1 spinal muscular atrophy
Authors: Buonsenso Danilo , Berti Beatrice , Palermo Concetta , Leone Daniela , Ferrantini Gloria , De Sanctis Roberto , Onesimo Roberta , Curatola Antonietta , Fanelli Lavinia , Forcina Nicola , Norcia Giulia , Carnicella Sara , Lucibello Simona , Mercuri Eugenio , Pane Marika
Published: May 2020

Objective

To investigate ultrasound features of diaphragm motion and function in type 1 spinal muscular atrophy (SMA‐1) patients.

Design

Prospective study.

Patients

The study cohort included SMA‐1 children younger than 18‐year‐old. Control subjects included type 2 and type 3 SMA and other neuromuscular disorders younger than 18‐year‐old.

Methodology

Diaphragm ultrasound evaluating diaphragmatic excursion, speed of diaphragmatic contraction, duration of the respiratory cycle, inspiratory/expiratory relationship, end‐inspiratory and ‐expiratory thickness, thickening fraction, and pattern of contractility. The interrater reliability for each variable was established by calculation of Cohen's k coefficient.

Results

Twenty‐three SMA‐1 patients and 12 controls were evaluated. Diaphragm ultrasound values were within normal ranges in all study cohort patients and no difference was found with controls. There was a gradient of diaphragm function with SMA 1.9 subgroup having the best and SMA 1.1 having the worst parameters, particularly in end‐inspiratory thickness and diaphragmatic excursion (P = .031 and P = .041, respectively). Seventy‐four percent of SMA‐1 patients had a dysmotility pattern of diaphragm contraction, mostly represented in SMA 1.9 subgroup (P = .001). This pattern was observed in 92.8% of children on noninvasive ventilation (NIV) for less than 16 hours/d of and in 20% patients with invasive ventilation or NIV for more than 16 hours/d (P = .027). The dysmotility pattern was never observed in the control group. The levels of interobserver agreement were high for “diaphragm irregularities,” “inspiratory/expiratory relationship,” and “diaphragm thickness,” and good for the other variables.

Conclusions

Ultrasound can be used to evaluate diaphragm function and contractility in SMA‐1 children, providing additional information to the clinical examination and functional respiratory tests, describing a characteristic contractility pattern in these patients. Longitudinal studies are needed to understand the impact of diaphragm dysmotility and other parameters on long‐term outcome in SMA‐1 patients.
Dexamethasone or prednisolone for asthma exacerbations in children: A cost‐effectiveness analysis
Authors: Rodriguez‐Martinez Carlos E. , Sossa‐Briceño Monica P. , Castro‐Rodriguez Jose A.
Published: May 2020

Objectives

Although a short course (ie, 3 to 5 days) of orally administered prednisolone is a common and widely accepted practice among clinicians for administering systemic corticosteroids in pediatric acute asthma, oral dexamethasone for 1 to 2 days is an attractive alternative to prednisolone due to its better palatability and compliance. However, a cost‐effectiveness analysis regarding the use of dexamethasone compared to prednisolone is not sufficient, especially in lower‐ and middle‐income countries. The objective of this study was to analyze the cost‐effectiveness of prednisolone vs oral dexamethasone for treating pediatric asthma exacerbations.

Methods

Using a decision‐analysis model, we analyzed the cost‐effectiveness of prednisolone vs oral dexamethasone for treating acute pediatric asthma. Effectiveness parameters were derived from a systematic review of the published literature. Data for costs were acquired from hospital accounts and from an official national database, the national manual of drug prices in Colombia. The study was carried out from a Colombian third‐party payer perspective. The principal outcome of the model was the avoidance of hospitalization.

Results

The base‐case analysis showed that compared to dexamethasone, administering prednisolone was associated with lower overall treatment costs (US$93.97 vs US$104.91 mean cost per patient) without a significant difference in the probability of hospitalization avoided (.9108 vs .9108).

Conclusions

The present study shows that in Colombia, a middle‐income country, compared with oral dexamethasone, the use of prednisolone for treating acute pediatric asthma is cost‐effective, yielding a similar probability of hospitalization at lesser overall costs.
Evolutionary model of protein secondary structure capable of revealing new biological relationships
Authors: Lai Jhih‐Siang , Rost Burkhard , Kobe Bostjan , Bodén Mikael
Published: May 2020

Ancestral sequence reconstruction has had recent success in decoding the origins and the determinants of complex protein functions. However, phylogenetic analyses of remote homologues must handle extreme amino acid sequence diversity resulting from extended periods of evolutionary change. We exploited the wealth of protein structures to develop an evolutionary model based on protein secondary structure. The approach follows the differences between discrete secondary structure states observed in modern proteins and those hypothesized in their immediate ancestors. We implemented maximum likelihood‐based phylogenetic inference to reconstruct ancestral secondary structure. The predictive accuracy from the use of the evolutionary model surpasses that of comparative modeling and sequence‐based prediction; the reconstruction extracts information not available from modern structures or the ancestral sequences alone. Based on a phylogenetic analysis of a sequence‐diverse protein family, we showed that the model can highlight relationships that are evolutionarily rooted in structure and not evident in amino acid‐based analysis.
Likelihood‐based inference for a frailty‐copula model based on competing risks failure time data
Authors: Wang Yin‐Chen , Emura Takeshi , Fan Tsai‐Hung , Lo Simon M.S. , Wilke Ralf Andreas
Published: May 2020

A competing risks phenomenon arises in industrial life tests, where multiple types of failure determine the working duration of a unit. To model dependence among marginal failure times, copula models and frailty models have been developed for competing risks failure time data. In this paper, we propose a frailty‐copula model, which is a hybrid model including both a frailty term (for heterogeneity among units) and a copula function (for dependence between failure times). We focus on models that are useful to investigate the reliability of marginal failure times that are Weibull distributed. Furthermore, we develop likelihood‐based inference methods based on competing risks data, including accelerated failure time models. We also develop a model‐diagnostic procedure to assess the adequacy of the proposed model to a given dataset. Simulations are conducted to demonstrate the operational performance of the proposed methods, and a real dataset is analyzed for illustration. We make an R package “gammaGumbel” such that users can apply the suggested statistical methods to their data.