bluuebunny/crossref_metadata_2025_split huggingface dataset:
QIIME 2 Enables Comprehensive End‐to‐End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data
Authors: Estaki Mehrbod , Jiang Lingjing , Bokulich Nicholas A. , McDonald Daniel , González Antonio , Kosciolek Tomasz , Martino Cameron , Zhu Qiyun , Birmingham Amanda , Vázquez‐Baeza Yoshiki , Dillon Matthew R. , Bolyen Evan , Caporaso J. Gregory , Knight Rob 
Published: April 2020

AbstractQIIME 2 is a completely re‐engineered microbiome bioinformatics platform based on the popular QIIME platform, which it has replaced. QIIME 2 facilitates comprehensive and fully reproducible microbiome data science, improving accessibility to diverse users by adding multiple user interfaces. QIIME 2 can be combined with Qiita, an open‐source web‐based platform, to re‐use available data for meta‐analysis. The following basic protocol describes how to install QIIME 2 on a single computer and analyze microbiome sequence data, from processing of raw DNA sequence reads through generating publishable interactive figures. These interactive figures allow readers of a study to interact with data with the same ease as its authors, advancing microbiome science transparency and reproducibility. We also show how plug‐ins developed by the community to add analysis capabilities can be installed and used with QIIME 2, enhancing various aspects of microbiome analyses—e.g., improving taxonomic classification accuracy. Finally, we illustrate how users can perform meta‐analyses combining different datasets using readily available public data through Qiita. In this tutorial, we analyze a subset of the Early Childhood Antibiotics and the Microbiome (ECAM) study, which tracked the microbiome composition and development of 43 infants in the United States from birth to 2 years of age, identifying microbiome associations with antibiotic exposure, delivery mode, and diet. For more information about QIIME 2, see https://qiime2.org. To troubleshoot or ask questions about QIIME 2 and microbiome analysis, join the active community at https://forum.qiime2.org. © 2020 The Authors.Basic Protocol: Using QIIME 2 with microbiome dataSupport Protocol: Further microbiome analyses
Liquid Chromatography–Mass Spectrometry (LC‐MS)‐Based Analysis for Lipophilic Compound Profiling in Plants
Authors: Lapidot‐Cohen Taly , Rosental Leah , Brotman Yariv 
Published: April 2020

AbstractLipids are fascinating due to their chemical diversity, which is especially vast in the plant kingdom thanks to the high plasticity of the plant biosynthetic machinery. Lipidomic studies aim to simultaneously analyze a large number of lipid compounds of diverse classes in a given sample. The method presented here uses liquid chromatography–mass spectrometry (LC‐MS)‐based lipidomic profiling in a relatively fast, robust, and high‐throughput manner for high‐coverage quantification and annotation of lipophilic compounds. Protocols cover sample preparation, LC‐MS‐based measurement, and data extraction and annotation. An extensive lipid library for triacylglycerols, galactolipids, and phospholipids is provided. The extended profiling described here could be used in a range of applications and is suitable for integration with other omic datasets. © 2020 by John Wiley & Sons, Inc.Basic Protocol 1: Sample preparation and metabolite extractionBasic Protocol 2: Liquid chromatography–mass spectrometry (LC‐MS) analysisBasic Protocol 3: Data extraction, annotation, and quantification
Comparative photosynthesis physiology of cultivated and wild lettuce under control and low‐water stress
Authors: Eriksen Renée L. , Adhikari Neil D. , Mou Beiquan 
Published: April 2020

AbstractLettuce (Lactuca sativa L.) is an important vegetable crop; however, increased demand and reduced recharge to the aquifer systems in the major field growing regions are making irrigation requirements more difficult and costly to meet. If lettuce production is to be sustainable in these regions, there is a need to breed varieties with higher water use efficiency (WUE) that produce similar biomass under reduced irrigation. The wild progenitor of lettuce, Lactuca serriola L., is a common, ruderal weed that is generally considered more drought tolerant than its cultivated relative. We compared the photosynthetic physiology of two representative accessions of these species under progressive low‐water stress for 10 d and observed that leaf intrinsic WUE was higher under moderate low‐water stress in L. serriola acc. US96UC23 than lettuce cultivar ‘Salinas’. Carbon assimilation (A) and carboxylating efficiency was generally higher in US96UC23 under control water treatments, which we determine to be due to higher mesophyll conductance (gm). No differences were observed between the two species in concentrations of the carboxylating enzyme Rubisco. We find mesophyll limitations to be the most significant relative limiting factor in Salinas. The domestication of cultivated lettuce from this wild relative involved intensive morphological alteration of the leaf, which appears to have led to significantly reduced gm and, concomitantly, A. Breeding for improved gm in lettuce may lead to increases in A and WUE under moderate low‐water stress.
Predicting a comprehensive operationalization of eating disorder recovery: Examining self‐concept, personality, and negative affect
Authors: Bardone‐Cone Anna M. , Miller Alexandra J. , Thompson Katherine A. , Walsh Emily C. 
Published: April 2020

AbstractObjectiveOur goal was to examine potential predictors of a comprehensive operationalization of eating disorder recovery, characterized by physical, behavioral, and cognitive recovery, focusing on constructs related to self‐concept, personality, and negative affect.MethodParticipants were women with a history of an eating disorder who provided data via survey and interview at two time points separated by about 7–8 years and who met criteria for an eating disorder diagnosis at baseline (N = 36).ResultsLogistic regression models revealed that self‐esteem was a significant predictor of recovery status (OR = 1.12, p = .039) such that individuals with higher self‐esteem at baseline demonstrated significantly greater odds of being in full recovery at follow‐up. However, when self‐esteem was considered in a set along with baseline imposter phenomenon and anxiety, no single construct emerged as a significant unique predictor of recovery in logistic regression analyses.DiscussionThese results highlight the potential importance of self‐esteem in relation to recovery, with clinical implications related to bolstering self‐esteem as part of eating disorder treatment. Future research should continue to explore predictors using a comprehensive operationalization of eating disorder recovery in larger, more diverse samples to optimally identify factors associated with achieving recovery.
Idiopathic giant cell myocarditis or cardiac sarcoidosis? A retrospective audit of a nationwide case series
Authors: Ekström Kaj , Räisänen‐Sokolowski Anne , Lehtonen Jukka , Nordenswan Hanna‐Kaisa , Mäyränpää Mikko I. , Kupari Markku 
Published: April 2020

AbstractAimsCardiac sarcoidosis (CS) and giant cell myocarditis (GCM) are inflammatory cardiomyopathies sharing histopathological and clinical features. Their differentiation is difficult and susceptible of confusion and apparent mistakes. The possibility that they represent different phenotypes of a single disease has been debated.Methods and resultsWe made a retrospective audit of 73 cases of GCM diagnosed in Finland since the late 1980s. All available histological material was reanalyzed as were other examinations pertinent to the distinction between GCM and CS. Finding granulomas in or outside the heart was considered diagnostic of CS and exclusive of GCM. Altogether 45 of the 73 cases of GCM (62%) were reclassified as CS. In all except one case, this was based on finding sarcoid granulomas that either had been originally missed (n = 29) or misinterpreted (n = 11) or were found in additional posttransplant myocardial specimens (n = 3) or samples of extracardiac tissue (n = 1) accrued over the disease course. Supporting the reclassification, patients relocated to the CS group had less heart failure at presentation (prevalence 20% vs. 46%, P = 0.017) and better 1 year transplant‐free survival (82% vs. 45%, P = 0.011) than patients considered to represent true GCM.ConclusionsRecognizing granulomas in or outside the heart remains a challenge for the pathologist. Given that CS and GCM are considered distinct diseases and granulomas exclusive of GCM, many cases of GCM, if thoroughly scrutinized, may need reclassification as CS. However, whether CS and GCM are truly different entities or parts of a one‐disease continuum has not yet been conclusively settled.
Systematic review of Internet of Things in smart farming
Authors: Terence Sebastian , Purushothaman Geethanjali 
Published: April 2020

ABSTRACTAgriculture unquestionably is one of the traditional occupations, which feeds all mankind in the world. Continuous changes are happening in the agricultural field to increase production. Researchers are applying various techniques to improve farming methods. To monitor plants even from remote places and to improve the yield of plants, Internet of Things (IoT), which is a boon in today's world, is applied in farming, in general, known as smart farming. Smart farming is a way where the farmers can monitor their field and manage farming activities from remote places. This reduces man power and increases resource utilization in farming. In this article, we have studied the architecture of smart farming and studied different smart farming techniques, also we have classified smart farming techniques into three categories, namely, IoT‐based agricultural monitoring and controlling system, automatic irrigation system, and plant disease monitoring system. The review for the article is selected based on the systematic literature review method, and articles published from 2011 to 2019 are considered for review. Different IoT technologies such as sensors, gateway, communication system, user interface and experiment nature, plant type, disease type, advantages, and limitations are also reviewed. Future research direction and challenges in smart farming techniques are also discussed.
Changing practice patterns in head and neck oncologic surgery in the early COVID‐19 era
Authors: Kiong Kimberley L. , Guo Theresa , Yao Christopher M. K. L. , Gross Neil D. , Hanasono Matthew M. , Ferrarotto Renata , Rosenthal David I. , Myers Jeffrey N. , Hanna Ehab Y. , Lai Stephen Y. 
Published: April 2020

AbstractBackgroundThe novel coronavirus 2019 (COVID‐19) pandemic has changed health care, challenged by resource constraints and fears of transmission. We report the surgical practice pattern changes in a Head and Neck Surgery department of a tertiary cancer care center and discuss the issues surrounding multidisciplinary care during the pandemic.MethodsWe report data regarding outpatient visits, multidisciplinary treatment planning conference, surgical caseload, and modifications of oncologic therapy during this pandemic and compared this data to the same interval last year.ResultsWe found a 46.7% decrease in outpatient visits and a 46.8% decrease in surgical caseload, compared to 2019. We discuss the factors involved in the decision‐making process and perioperative considerations.ConclusionsSurgical practice patterns in head and neck oncologic surgery will continue to change with the evolving pandemic. Despite constraints, we strive to prioritize and balance the oncologic and safety needs of patients with head and neck cancer in the face of COVID‐19.
Objective evaluation of anosmia and ageusia in COVID‐19 patients: Single‐center experience on 72 cases
Authors: Vaira Luigi Angelo , Deiana Giovanna , Fois Alessandro Giuseppe , Pirina Pietro , Madeddu Giordano , De Vito Andrea , Babudieri Sergio , Petrocelli Marzia , Serra Antonello , Bussu Francesco , Ligas Enrica , Salzano Giovanni , De Riu Giacomo 
Published: April 2020

AbstractBackgroundThe first European case series are detecting a very high frequency of chemosensitive disorders in COVID‐19 patients, ranging between 19.4% and 88%.MethodsOlfactory and gustatory function was objectively tested in 72 COVID‐19 patients treated at University Hospital of Sassari.ResultsOverall, 73.6% of the patients reported having or having had chemosensitive disorders. Olfactory assessment showed variable degree hyposmia in 60 cases and anosmia in two patients. Gustatory assessment revealed hypogeusia in 33 cases and complete ageusia in one patient. Statistically significant differences in chemosensitive recovery were detected based on age and distance from the onset of clinical manifestations.ConclusionOlfactory and gustatory dysfunctions represent common clinical findings in COVID‐19 patients. Otolaryngologists and head‐neck surgeons must by now keep this diagnostic option in mind when evaluating cases of ageusia and nonspecific anosmia that arose suddenly and are not associated with rhinitis symptoms.
Overview of COVID‐19 testing and implications for otolaryngologists
Authors: Vinh Daniel B. , Zhao Xiao , Kiong Kimberley L. , Guo Theresa , Jozaghi Yelda , Yao Chris , Kelley James M. , Hanna Ehab Y. 
Published: April 2020

AbstractBackgroundTesting for SARS‐CoV‐2 is important for decision making prior to surgery in otolaryngology. An understanding of current and developing testing methods is important for interpreting test results.MethodsWe performed a literature review of current evidence surrounding SARS‐CoV‐2 diagnostic testing highlighting its utility, limitations, and implications for otolaryngologists.ResultsThe currently accepted RT‐PCR test for SARS‐CoV‐2 has varying sensitivity according to which subsite of the aerodigestive tract is sampled. Nasal swab sensitivities appear to be about 70%. Chest CT imaging for screening purposes is not currently recommended.ConclusionDue to the current sensitivity of RT‐PCR based testing for SARS‐CoV‐2, a negative test cannot rule out COVID‐19. Full PPE should be worn during high‐risk procedures such as aerosol generating procedures even if testing is negative. Patients who test positive during screening should have their surgeries postponed if possible until asymptomatic and have tested negative for SARS‐CoV‐2.
Respiratory and pulmonary complications in head and neck cancer patients: Evidence‐based review for the COVID‐19 era
Authors: Silverman Dustin A. , Lin Chen , Tamaki Akina , Puram Sidharth V. , Carrau Ricardo L. , Seim Nolan B. , Eskander Antoine , Rocco James W. , Old Matthew O. , Kang Stephen Y. 
Published: April 2020

AbstractBackgroundPulmonary complications and infections frequently affect patients with head and neck squamous cell carcinoma (HNSCC). Common characteristics can predispose these patients to the development of severe respiratory illness, which may be particularly relevant during the 2019 coronavirus disease (COVID‐19) pandemic.MethodsA scoping review was performed to assess the impact of pulmonary comorbidities and adverse respiratory outcomes in HNSCC patients.ResultsAdvanced age, history of tobacco and alcohol abuse, and cardiopulmonary comorbidities are significant risk factors for the development of adverse respiratory outcomes. Treatment toxicities from radiation or chemoradiation therapy significantly increase these risks.ConclusionRespiratory complications are a frequent cause of morbidity and mortality among HNSCC patients, and the COVID‐19 pandemic may disproportionately affect this population. Interventions designed to decrease smoking and alcohol use, improve oral hygiene, and aggressively manage medical comorbidities are important to the long‐term management and health of these patients.
Analysis of copy number variation by sequencing in fetuses with nuchal translucency thickening
Authors: Lan Liubing , Wu Heming , She Lingna , Zhang Bosen , He Yanhong , Luo Dandan , Wang Huaxian , Zheng Zhiyuan 
Published: April 2020

AbstractObjectiveCopy number variation sequencing (CNV‐seq) technique was used to analyze the genetic etiology of fetuses with increased nuchal translucency (NT).MethodsA total of 139 women with gestational 11‐14 weeks whose fetuses were detected with increased NT (NT ≥ 2.5 mm) in our hospital from July 2016 to December 2018 were selected. Fetal specimens were performed for karyotyping analysis and CNV sequencing.ResultsAccording to the nuchal translucency thickness, 2.5‐3.4, 3.5‐4.4, 4.5‐5.4, and more than 5.5 mm, the rates of chromosomal abnormalities were 22.8% (13/57), 30.8% (12/39), 42.1% (8/19), and 62.5% (15/24), respectively. There was significant difference among the incidences of chromosomal abnormalities in four groups (χ2 = 37.69, P < .01) and the incidences increased with fetal NT thickness. Among 139 cases, there were 36 cases (25.9%) with abnormal chromosome karyotypes. Meanwhile, there were 45 cases (32.3%) with abnormal CNV. In the 12 cases with abnormal CNV and normal chromosome karyotypes, there were 2 cases of pathogenic CNV, 7 cases of CNV with unknown clinical significance, and 3 cases of possibly benign CNV. There was no significant difference in CNV between pregnant women in advanced maternal age and those in normal maternal age (χ2 = 1.389, P = .239). In the fetus who showed abnormalities in NT and ultrasonography (χ2 = 5.13, P < .05) and the fetus aborted (χ2 = 113.19, P < .05), the abnormal rate of CNV was higher with statistically significant difference.ConclusionCNV‐seq combined karyotype analysis should be performed simultaneously in fetuses with increased NT, providing a basis for genetic counseling, which is of great significance for prenatal diagnosis.
Is a Fetal Echocardiography Necessary in IVF‐ICSI Pregnancies After Anatomic Survey?
Authors: Aderibigbe Oluyemi A. , Ranzini Angela C. 
Published: April 2020

AbstractPurposeIn vitro fertilization with intracytoplasmic sperm injection (IVF‐ICSI) is generally regarded as an indication for fetal echocardiography due to a reported increased risk of congenital abnormalities including cardiac anomalies. In this study we evaluated the utility of fetal echocardiography after anatomic survey in an experienced center.MethodsThis was a retrospective case review of in vitro fertilization with intracytoplasmic sperm injection pregnancies who had echocardiography in our institution from January 1996 to October 2010.ResultsRecords from 85 mothers and 110 fetuses were identified. During anatomic survey, six cardiac anomalies were identified, including four ventricular septal defects, one pulmonary‐aortic disproportion, and one post‐valvular pulmonary artery dilatation. At fetal echocardiography, two of the four ventricular septal defects were confirmed and an additional three were identified. The most common cardiac anomaly seen in our population of IVF‐ICSI pregnancies was ventricular septal defect, which was identified in 3.6% of all cases in the neonatal period. Of ventricular septal defects identified in the prenatal period, 71% resolved before birth.ConclusionIn experienced centers, a fetal echocardiography may not be necessary if the 3 vessels tracheal view of the heart is evaluated and the heart is evaluated carefully for a ventricular septal defect.
Long‐term coexistence of SARS‐CoV‐2 with antibody response in COVID‐19 patients
Authors: Wang Bin , Wang Li , Kong Xianggen , Geng Jin , Xiao Di , Ma Chunhong , Jiang Xue‐Mei , Wang Pei‐Hui 
Published: April 2020

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection causing coronavirus disease 2019 (COVID‐19) has spread worldwide. Whether antibodies are important for the adaptive immune responses against SARS‐CoV‐2 infection needs to be determined. Here, 26 cases of COVID‐19 in Jinan, China, were examined and shown to be mild or with common clinical symptoms, and no case of severe symptoms was found among these patients. Strikingly, a subset of these patients had SARS‐CoV‐2 and virus‐specific IgG coexist for an unexpectedly long time, with two cases for up to 50 days. One COVID‐19 patient who did not produce any SARS‐CoV‐2–bound IgG successfully cleared SARS‐CoV‐2 after 46 days of illness, revealing that without antibody‐mediated adaptive immunity, innate immunity alone may still be powerful enough to eliminate SARS‐CoV‐2. This report may provide a basis for further analysis of both innate and adaptive immunity in SARS‐CoV‐2 clearance, especially in nonsevere cases.
Outcome in Caucasian patients with hepatitis B e antigen negative chronic infection: A long‐term observational cohort study
Authors: Koc Özgür M. , Robaeys Geert , Topal Halit , Bielen Rob , Busschots Dana , Fevery Johan , Koek Ger H. , Nevens Frederik 
Published: April 2020

AbstractSensitive polymerase chain reaction assays to measure hepatitis B virus (HBV) DNA became only available the last decade. Hence, the long‐term outcome of Caucasian patients in Western Europe with hepatitis B e antigen (HBeAg)‐negative chronic infection, especially with a baseline HBV DNA level ⩾2000 IU/mL, is still unclear. Out of a cohort of 1936 chronic HBV patients, 413 Caucasian individuals were identified with HBeAg‐negative chronic infection, defined as persistently normal alanine aminotransferase (ALT) levels and HBV DNA levels <20 000 IU/mL. During a mean follow‐up of 12 years, 366 (88.6%) maintained an HBeAg‐negative chronic infection status, whereas 25 (6.1%) developed chronic active hepatitis (CAH). In total, Nine of these 25 CAH cases were related to immunosuppression. In total, 22 (5.3%) individuals had ALT > 2 × upper limit of normal due to non‐HBV‐related causes. The cumulative probability of spontaneously developing CAH after 10 years was almost exclusively seen in patients with baseline HBV DNA level ⩾2000 IU/mL (11.7% vs 1.2%; P < .001). Advanced liver disease developed significantly more in patients with baseline HBV DNA level ⩾2000 IU/mL (5.2% vs 1.5%; P = .018) and occurred especially in patients with obesity (16.7% vs 4.2%; P = .049). The incidence of hepatocellular carcinoma was 0.0%. Caucasian patients with HBeAg‐negative chronic infection and baseline HBV DNA level <2000 IU/mL have an excellent long‐term prognosis in the absence of immunosuppressive therapy. However, patients with baseline HBV DNA level ⩾2000 IU/mL are at risk to develop advanced liver disease.
Fatty Acids of Microbial Origin in the Perirenal Fat of Rats (Rattus norvegicus domestica) and Guinea Pigs (Cavia porcellus) Fed Various Diets
Authors: De Cuyper Annelies , Winkler Daniela , Tütken Thomas , Janssens Geert P.J. , Clauss Marcus 
Published: April 2020

AbstractGuinea pigs are assumed to practice caecotrophy to a higher degree than rats. Studies from leporids suggest that through the practice of caecotrophy, hindgut fermenting species could build up microbial fatty acids (FA) in body tissues. We hypothesized that microbial FA would be detectable in the body tissue of guinea pigs and rats, and this to a higher degree in guinea pigs. Twenty‐four rats and guinea pigs were fed with four different pelleted diets (lucerne‐, meat‐, meat‐bone‐, insect‐based) in groups of six animals for 8 weeks. Perirenal adipose tissue differed in FA composition between the species in spite of the common diets. FA typically associated with microbial activity (saturated FA (SFA; typically 18:0), monounsaturated FA (MUFA; typically trans‐fatty acids TFA), and odd‐ and branched‐chain FA (Iso‐FA)), were all detected. Guinea pigs had higher SFA levels than rats except on the lucerne diet. Concentrations of 18:0 were higher for guinea pigs on the meat and bone diet. Iso‐FA concentrations in guinea pigs exceeded those of rats on all diets. FA profiles with a microbial fingerprint appear—although in low proportions—in the body tissue of both species, and this seemingly to a higher extent in guinea pigs. With respect to whether consumption of rodent meat rich in microbial FA has particular effects on human health as shown for ruminant products, microbial FA concentrations are probably too low to cause any distinct effects.