bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phenotyping analysis of maize stem using micro-computed tomography at the elongation and tasseling stages
Authors: Zhang Ying , Ma Liming , Wang Jinglu , Wang Xiaodong , Guo Xinyu , Du Jianjun 
Published: January 2020

Abstract
Background
Micro-computed tomography (μCT) bring a new opportunity to accurately quantify micro phenotypic traits of maize stem, also provide comparable benchmark to evaluate its dynamic development at the different growth stages. The progressive accumulation of stem biomass brings manifest structure changes of maize stem and vascular bundles, which are closely related with maize varietal characteristics and growth stages. Thus, micro-phenotyping (μPhenotyping) of maize stems is not only valuable to evaluate bio-mechanics and water-transport performance of maize, but also yield growth-based traits for quantitative traits loci (QTL) and functional genes location in molecular breeding.

Result
In this study, maize stems of 20 maize cultivars and two growth stages were imaged using μCT scanning technology. According to the observable differences of maize stems from the elongation and tasseling stages, function zones of maize stem were firstly defined to describe the substance accumulation of maize stems. And then a set of image-based μPhenotyping pipelines were implemented to quantify maize stem and vascular bundles at the two stages. The coefficient of determination (R2) of counting vascular bundles was higher than 0.95. Based on the uniform contour representation, intensity-related, geometry-related and distribution-related traits of vascular bundles were respectively evaluated in function zones and structure layers. And growth-related traits of the slice, epidermis, periphery and inner zones were also used to describe the dynamic growth of maize stem. Statistical analysis demonstrated the presented method was suitable to the phenotyping analysis of maize stem for multiple growth stages.

Conclusions
The novel descriptors of function zones provide effective phenotypic references to quantify the differences between growth stages; and the detection and identification of vascular bundles based on function zones are more robust to determine the adaptive image analysis pipeline. Developing robust and effective image-based phenotyping method to assess the traits of stem and vascular bundles, is highly relevant for understanding the relationship between maize phenomics and genomics.
Non-parametric correction of estimated gene trees using TRACTION
Authors: Christensen Sarah , Molloy Erin K. , Vachaspati Pranjal , Yammanuru Ananya , Warnow Tandy 
Published: January 2020

Abstract
Motivation
Estimated gene trees are often inaccurate, due to insufficient phylogenetic signal in the single gene alignment, among other causes. Gene tree correction aims to improve the accuracy of an estimated gene tree by using computational techniques along with auxiliary information, such as a reference species tree or sequencing data. However, gene trees and species trees can differ as a result of gene duplication and loss (GDL), incomplete lineage sorting (ILS), and other biological processes. Thus gene tree correction methods need to take estimation error as well as gene tree heterogeneity into account. Many prior gene tree correction methods have been developed for the case where GDL is present.

Results
Here, we study the problem of gene tree correction where gene tree heterogeneity is instead due to ILS and/or HGT. We introduce TRACTION, a simple polynomial time method that provably finds an optimal solution to the RF-optimal tree refinement and completion (RF-OTRC) Problem, which seeks a refinement and completion of a singly-labeled gene tree with respect to a given singly-labeled species tree so as to minimize the Robinson−Foulds (RF) distance. Our extensive simulation study on 68,000 estimated gene trees shows that TRACTION matches or improves on the accuracy of well-established methods from the GDL literature when HGT and ILS are both present, and ties for best under the ILS-only conditions. Furthermore, TRACTION ties for fastest on these datasets. We also show that a naive generalization of the RF-OTRC problem to multi-labeled trees is possible, but can produce misleading results where gene tree heterogeneity is due to GDL.
Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels
Authors: Alam Mohammad Tauqeer , Amos Gregory C. A. , Murphy Andrew R. J. , Murch Simon , Wellington Elizabeth M. H. , Arasaradnam Ramesh P. 
Published: January 2020

Abstract
Background
Inflammatory bowel disease (IBD), is a debilitating group of chronic diseases including Crohn’s Disease (CD) and ulcerative colitis (UC), which causes inflammation of the gut and affects millions of people worldwide. At different taxonomic levels, the structure of the gut microbiota is significantly altered in IBD patients compared to that of healthy individuals. However, it is unclear how these IBD-affected bacterial groups are related to other common bacteria in the gut, and how they are connected across different disease conditions at the global scale.

Results
In this study, using faecal samples from patients with IBD, we show through diversity analysis of the microbial community structure based on the 16S rRNA gene that the gut microbiome of IBD patients is less diverse compared to healthy individuals. Furthermore, we have identified which bacterial groups change in abundance in both CD and UC compared to healthy controls. A substantial imbalance was observed across four major bacterial phyla including Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria, which together constitute > 98% of the gut microbiota. Next, we reconstructed a bacterial family co-abundance network based on the correlation of abundance profiles obtained from the public gut microbiome data of > 22,000 samples of faecal and gut biopsies taken from both diseased and healthy individuals. The data was compiled using the EBI metagenomics database (Mitchell et al. in Nucleic Acids Res 46:D726–D735, 2018). By mapping IBD-altered bacterial families to the network, we show that the bacterial families which exhibit an increased abundance in IBD conditions are not well connected to other groups, implying that these families generally do not coexist together with common gut organisms. Whereas, the bacterial families whose abundance is reduced or did not change in IBD conditions compared to healthy conditions are very well connected to other bacterial groups, suggesting they are highly important groups of bacteria in the gut that can coexist with other bacteria across a range of conditions.

Conclusions
IBD patients exhibited a less diverse gut microbiome compared to healthy individuals. Bacterial groups which changed in IBD patients were found to be groups which do not co-exist well with common commensal gut bacteria, whereas bacterial groups which did not change in patients with IBD were found to commonly co-exist with commensal gut microbiota. This gives a potential insight into the dynamics of the gut microbiota in patients with IBD.
Sleep dysregulation, memory impairment, and CSF biomarkers during different levels of neurocognitive functioning in Alzheimer’s disease course
Authors: Liguori Claudio , Placidi Fabio , Izzi Francesca , Spanetta Matteo , Mercuri Nicola Biagio , Di Pucchio Alessandra 
Published: January 2020

Abstract
Background
Alzheimer's disease (AD) is frequently accompanied by sleep impairment, which can induce AD-related neurodegeneration. We herein investigated the sleep architecture, cognition, and cerebrospinal fluid (CSF) biomarkers (tau proteins and β-amyloid42) during AD progression from subjective cognitive impairment (SCI) to mild cognitive impairment (MCI) and eventually to AD dementia, and compared the results with cognitively normal (CN) subjects.

Methods
We included patients affected by SCI, MCI, mild AD, and moderate-to-severe AD in our study along with CN subjects as controls. All the subjects underwent nocturnal polysomnography to investigate sleep, neuropsychological testing to evaluate cognition, and lumbar puncture for CSF AD biomarkers assessment.

Results
Sleep (both rapid eye movement (REM) and non-REM sleep) and memory function are both progressively impaired during the course of AD from SCI to mild and subsequently to moderate AD. Further, sleep dysregulation appears earlier than cognitive deterioration, with a reduction of CSF β-amyloid42 level.

Conclusion
Sleep, memory, and CSF AD biomarkers are closely interrelated in AD progression from the earliest asymptomatic and preclinical stages of the disease related in AD since the earliest and preclinical stages of the disease.
Clinical significance of focal ß-amyloid deposition measured by 18F-flutemetamol PET
Authors: Kim Si Eun , Lee Byungju , Park Seongbeom , Cho Soo Hyun , Kim Seung Joo , Kim Yeshin , Jang Hyemin , Jeong Jee Hyang , Yoon Soo Jin , Park Kyung Won , Kim Eun-Joo , Jung Na Yeon , Yoon Bora , Jang Jae-Won , Hong Jin Yong , Hwang Jihye , Na Duk L. , Seo Sang Won , Choi Seong Hye , Kim Hee Jin 
Published: January 2020

Abstract
Background
Although amyloid PET of typical Alzheimer’s disease (AD) shows diffuse ß-amyloid (Aß) deposition, some patients show focal deposition. The clinical significance of this focal Aß is not well understood. We examined the clinical significance of focal Aß deposition in terms of cognition as well as Aß and tau cerebrospinal fluid (CSF) levels. We further evaluated the order of Aß accumulation by visual assessment.

Methods
We included 310 subjects (125 cognitively unimpaired, 125 mild cognitive impairment, and 60 AD dementia) from 9 referral centers. All patients underwent neuropsychological tests and 18F-flutemetamol (FMM) PET. Seventy-seven patients underwent CSF analysis. Each FMM scan was visually assessed in 10 regions (frontal, precuneus and posterior cingulate, lateral temporal, parietal, and striatum of each hemisphere) and was classified into three groups: No-FMM, Focal-FMM (FMM uptake in 1–9 regions), and Diffuse-FMM (FMM uptake in all 10 regions).

Results
53/310 (17.1%) subjects were classified as Focal-FMM. The cognitive level of the Focal-FMM group was better than that of Diffuse-FMM group and worse than that of No-FMM group. Among the Focal-FMM group, those who had FMM uptake to a larger extent or in the striatum had worse cognitive levels. Compared to the Diffuse-FMM group, the Focal-FMM group had a less AD-like CSF profile (increased Aß42 and decreased t-tau, t-tau/Aß42). Among the Focal-FMM group, Aß deposition was most frequently observed in the frontal (62.3%) and least frequently observed in the striatum (43.4%) and temporal (39.6%) regions.

Conclusions
We suggest that focal Aß deposition is an intermediate stage between no Aß and diffuse Aß deposition. Furthermore, among patients with focal Aß deposition, those who have Aß to a larger extent and striatal involvement show clinical features close to diffuse Aß deposition. Further longitudinal studies are needed to evaluate the disease progression of patients with focal Aß deposition.
Laryngeal polyp associated with reflux disease: a case report
Authors: Hassan Wael Abdo 
Published: January 2020

Abstract
Background
Among the most common benign laryngeal lesions are vocal nodules and polyps. Their etiology is related to vocal abuse. Gastroesophageal reflux disease is a common condition presenting with a broad spectrum of symptoms, among which are extraesophageal manifestations such as laryngeal polyps.

Case presentation
A 24-year-old Middle Eastern woman presented to the author’s institution with dysphonia and dyspepsia. She underwent endoscopy and was diagnosed with severe reflux disease. In addition, laryngoscopy revealed a polyp at the left vocal cord, and the patient underwent polypectomy. Histopathological examination revealed a laryngeal polyp of telangiectatic type characterized by hyperplastic epithelial covering with reactive atypia, prominent superficial acanthosis with neutrophils, and prominent chronic inflammation and thrombosed vessels in the stroma.

Conclusion
This report focuses on the pathological findings associated with a laryngeal polyp in a young patient diagnosed with severe reflux disease. Acknowledging such characteristic changes in a laryngeal polyp could aid in the diagnosis of gastroesophageal reflux disease.
Toxicity management of regorafenib in patients with gastro-intestinal stromal tumour (GIST) in a tertiary cancer centre
Authors: Chamberlain Florence , Farag Sheima , Williams-Sharkey Constance , Collingwood Cecilia , Chen Lucia , Mansukhani Sonia , Engelmann Bodil , Al-Muderis Omar , Chauhan Dharmisha , Thway Khin , Fisher Cyril , Jones Robin L. , Gennatas Spyridon , Benson Charlotte 
Published: January 2020

Abstract
Background
Regorafenib is a multi-kinase inhibitor approved as third line treatment for metastatic GIST. Dose limiting toxicities are frequently seen and many patients require dose reductions. This study aimed to evaluate regorafenib toxicities and their management in a real-world GIST population.

Methods
Retrospective review of a prospectively maintained database identified 50 patients with GIST treated with regorafenib at our centre between March 2013 and September 2018.

Results
Median progression free survival (PFS) was 7.7 months [interquartile range (IQR) 2.8–14.4 months]. Median overall survival (OS) from start of regorafenib to death or last follow up was 15.7 months (IQR 9.2–28.4 months). Baseline median Eastern Cooperative Oncology Group (ECOG) performance status on starting regorafenib was 1. The main reason for discontinuing regorafenib was progressive disease (PD) (31/50 [62%]) rather than toxicity (10/50 [20%]). Grade 3–4 adverse events (AEs) were seen in 23/50 (46%) patients; palmar-plantar erythrodysesthesia (PPE) was most frequently seen (9/50 (18%)). Two patients died whilst on treatment with regorafenib from multi-organ failure secondary to sepsis (4%). Dose reductions were required in 19/50 patients (38%) and 8/50 (16%) patients started regorafenib at a lower dose band than the recommended dose (160 mg) due to comorbidities or concern over a higher individual risk of toxicity.

Conclusion
Although PD was the main reason for discontinuing treatment, toxicity management and dosing of regorafenib remains critical. Median duration of treatment was longer compared to previous studies suggesting a durable clinical benefit with regorafenib with rigorous toxicity management.
Viruses in the Built Environment (VIBE) meeting report
Authors: Prussin Aaron J. , Belser Jessica A. , Bischoff Werner , Kelley Scott T. , Lin Kaisen , Lindsley William G. , Nshimyimana Jean Pierre , Schuit Michael , Wu Zhenyu , Bibby Kyle , Marr Linsey C. 
Published: January 2020

Abstract
Background
During a period of rapid growth in our understanding of the microbiology of the built environment in recent years, the majority of research has focused on bacteria and fungi. Viruses, while probably as numerous, have received less attention. In response, the Alfred P. Sloan Foundation supported a workshop entitled “Viruses in the Built Environment (VIBE),” at which experts in environmental engineering, environmental microbiology, epidemiology, infection prevention, fluid dynamics, occupational health, metagenomics, and virology convened to synthesize recent advances and identify key research questions and knowledge gaps regarding viruses in the built environment.

Results
Four primary research areas and funding priorities were identified. First, a better understanding of viral communities in the built environment is needed, specifically which viruses are present and their sources, spatial and temporal dynamics, and interactions with bacteria. Second, more information is needed about viruses and health, including viral transmission in the built environment, the relationship between virus detection and exposure, and the definition of a healthy virome. The third research priority is to identify and evaluate interventions for controlling viruses and the virome in the built environment. This encompasses interactions among viruses, buildings, and occupants. Finally, to overcome the challenge of working with viruses, workshop participants emphasized that improved sampling methods, laboratory techniques, and bioinformatics approaches are needed to advance understanding of viruses in the built environment.

Conclusions
We hope that identifying these key questions and knowledge gaps will engage other investigators and funding agencies to spur future research on the highly interdisciplinary topic of viruses in the built environment. There are numerous opportunities to advance knowledge, as many topics remain underexplored compared to our understanding of bacteria and fungi.
Corrections officers’ knowledge and perspectives of maternal and child health policies and programs for pregnant women in prison
Authors: Pendleton Virginia , Saunders Jennifer B. , Shlafer Rebecca 
Published: January 2020

Abstract
Background
In response to the dramatic increase in the number of women incarcerated in the United States—and a growing awareness that a small proportion of women enter prison pregnant and have unique health needs—some prisons have implemented policies and programs to support pregnant women (defined here as maternal and child health [MCH] policies and programs). Corrections officers (COs) are key stakeholders in the successful implementation of prison policies and programs. Yet, little empirical research has examined prison COs’ knowledge and perspectives of MCH policies and programs, particularly the impact such policies and programs have on COs’ primary job responsibility of maintaining safety and security. The objective of this mixed-methods study was to understand COs’ knowledge and perspectives of MCH policies and programs in one state prison, with a specific emphasis on the prison’s pregnancy and birth support (doula) program.

Results
Thirty-eight COs at a single large, Midwestern women’s prison completed an online survey, and eight of these COs participated in an individual, in-person qualitative interview. Results indicated that COs’ perspectives on MCH policies and programs were generally positive. Most COs strongly approved of the prison’s doula program and the practice of not restraining pregnant women. COs reported that MCH policies and programs did not interfere, and in some cases helped, with their primary job task of maintaining safety and security.

Conclusions
Findings support expansion of MCH programs and policies in prisons, while underscoring the need to offer more CO training and to gather more CO input during program development and implementation. MCH services that provide support to pregnant women that are outside the scope of COs’ roles may help reduce CO job demands, improve facility safety, and promote maternal and child health.
Rapid determination of aminoglycosides in pharmaceutical preparations by electrospray ionization mass spectrometry
Authors: Jariwala Freneil B. , Hibbs John A. , Zhuk Iryna , Sukhishvili Svetlana A. , Attygalle Athula B. 
Published: January 2020

AbstractAminoglycosides are broad-spectrum antibiotics often employed to combat Gram-negative bacterial infections. A technique based on electrospray-ionization mass spectrometry (ESI-MS) was developed for rapid determination of aminoglycosides. This method, which does not require prior chromatographic separation, or derivatization and extensive sample preparation steps, was deployed to estimate gentamicin, tobramycin, and amikacin in pharmaceutical formulations. Upon gas-phase collisional activation, protonated gentamicin, tobramycin, and amikacin undergo a facile loss of their respective “C” ring moiety to produce characteristic ions of m/z 322, 324, and 425, respectively. The mass spectral peak intensities for these specific product ions were monitored either by a flow-injection analysis selected-ion monitoring (FIA-SIM) time-intensity method or by a mass spectrometric internal-standard method. The linear dynamic ranges of detection for both methods were evaluated to be 10–1000 ng/mL for gentamicin, 25–2500 ng/mL for tobramycin, and 10–1000 ng/mL for amikacin. The internal-standard mass spectrometric method afforded lower intra-day and inter-day variations (2.3–3.0% RSD) compared to those from FIA-SIM method (4.5–5.0% RSD). This method was applied as a potential alternative procedure to determine gentamicin in commercial pharmaceutical samples and to monitor the release of gentamicin from “self-defensive” tannic acid-based layer-by-layer films into phosphate buffer solutions at different pHs.
Global prevalence of hidradenitis suppurativa and geographical variation—systematic review and meta-analysis
Authors: Phan Kevin , Charlton Olivia , Smith Saxon D. 
Published: January 2020

Abstract
Background
There is a significant variation in the reported prevalence of hidradenitis suppurativa (HS), ranging from 0.03–4%. We hypothesized that this significant variation may be due to different prevalence rates of HS according to geographical location as well as sex.

Objective
We aimed to perform a meta-analysis to determine pooled overall prevalence of HS, prevalence stratified according to geographical region and sex.

Materials and methods
A systematic review was performed by searching Ovid Medline, PubMed, Cochrane Library, DARE, and Embase, from inception to August 2018. A systematic review and meta-analysis was performed according to PRISMA guidelines. A meta-analysis of proportions was performed to determined pooled prevalence rates, with meta-regression based on geographic region. Prevalence in males versus females was also performed according to region.

Results
The overall pooled prevalence rate was 0.3% (0.2–0.6%) based on 118,760,093 HS cases available. Subgroup analysis demonstrated prevalence differences, with the highest being in Europe 0.8% (0.5–1.3%), compared to the USA 0.2% (0.1–0.4%), Asia-Pacific 0.2% (0.01–2.2%), and South America 0.2% (0.01–0.9%). Prevalence in males was lower compared to females in the USA (OR 0.403, 95% CI 0.37–0.439, P < 0.001) as well as in Europe (OR 0.635, 95% CI 0.397–1.015, P = 0.08) but not in the Asia-Pacific region (OR 0.936, 95% CI 0.319–2.751, P = 0.78).

Conclusion
Prevalence of HS varies significantly according to the geographical population. This variation is likely attributed to different ethnicity distributions amongst different continents.

Level of evidence
III