bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlation between Organelle Genetic Variation and RNA Editing in Dinoflagellates Associated with the Coral Acropora digitifera
Authors: Shoguchi Eiichi , Yoshioka Yuki , Shinzato Chuya , Arimoto Asuka , Bhattacharya Debashish , Satoh Noriyuki 
Published: February 2020

Abstract
In order to develop successful strategies for coral reef preservation, it is critical that the biology of both host corals and symbiotic algae are investigated. In the Ryukyu Archipelago, which encompasses many islands spread over ∼500 km of the Pacific Ocean, four major populations of the coral Acropora digitifera have been studied using whole-genome shotgun (WGS) sequence analysis (Shinzato C, Mungpakdee S, Arakaki N, Satoh N. 2015. Genome-wide single-nucleotide polymorphism (SNP) analysis explains coral diversity and recovery in the Ryukyu Archipelago. Sci Rep. 5:18211.). In contrast, the diversity of the symbiotic dinoflagellates associated with these A. digitifera populations is unknown. It is therefore unclear if these two core components of the coral holobiont share a common evolutionary history. This issue can be addressed for the symbiotic algal populations by studying the organelle genomes of their mitochondria and plastids. Here, we analyzed WGS data from ∼150 adult A. digitifera, and by mapping reads to the available reference genome sequences, we extracted 2,250 sequences representing 15 organelle genes of Symbiodiniaceae. Molecular phylogenetic analyses of these mitochondrial and plastid gene sets revealed that A. digitifera from the southern Yaeyama islands harbor a different Symbiodiniaceae population than the islands of Okinawa and Kerama in the north, indicating that the distribution of symbiont populations partially matches that of the four host populations. Interestingly, we found that numerous SNPs correspond to known RNA-edited sites in 14 of the Symbiodiniaceae organelle genes, with mitochondrial genes showing a stronger correspondence than plastid genes. These results suggest a possible correlation between RNA editing and SNPs in the two organelle genomes of symbiotic dinoflagellates.
Relative Effectiveness of Influenza Vaccines Among the United States Elderly, 2018–2019
Authors: Izurieta Hector S , Chillarige Yoganand , Kelman Jeffrey , Wei Yuqin , Lu Yun , Xu Wenjie , Lu Michael , Pratt Douglas , Wernecke Michael , MaCurdy Thomas , Forshee Richard 
Published: February 2020

AbstractBackgroundStudies among individuals ages ≥65 years have found a moderately higher relative vaccine effectiveness (RVE) for the high-dose (HD) influenza vaccine compared with standard-dose (SD) products for most seasons. Studies during the A(H3N2)-dominated 2017–2018 season showed slightly higher RVE for the cell-cultured vaccine compared with SD egg-based vaccines. We investigated the RVE of influenza vaccines among Medicare beneficiaries ages ≥65 years during the 2018–2019 season.MethodsThis is a retrospective cohort study using inverse probability of treatment weighting and Poisson regression to evaluate RVE in preventing influenza hospital encounters.ResultsAmong 12 777 214 beneficiaries, the egg-based adjuvanted (RVE, 7.7%; 95% confidence interval [CI], 3.9%–11.4%) and HD (RVE, 4.9%; 95% CI, 1.7%–8.1%) vaccines were marginally more effective than the egg-based quadrivalent vaccines. The cell-cultured quadrivalent vaccine was not significantly more effective than the egg-based quadrivalent vaccine (RVE, 2.5%; 95% CI, −2.4% to 7.3%).ConclusionsWe did not find major effectiveness differences between licensed vaccines used among the elderly during the 2018–2019 season. Consistent with prior research, we found that the egg-based adjuvanted and HD vaccines were slightly more effective than the egg-based quadrivalent vaccines.
Tolerogenic properties of CD206+ macrophages appeared in the sublingual mucosa after repeated antigen-painting
Authors: Yang Yue , Nagai Shigenori , Kang Siwen , Xia Yulong , Kawano Yohei , Miyake Kensuke , Karasuyama Hajime , Azuma Miyuki 
Published: February 2020

Abstract
The sublingual mucosa (SLM) in the oral cavity is utilized as the site for sublingual immunotherapy to induce tolerance against allergens. We previously reported that CD206+ round-type macrophage-like cells were induced in the SLM after repeated antigen (e.g. cedar pollen or fluorescein isothiocyanate (FITC))-painting. In this study, we examined the phenotypic and functional properties of CD206+ cells induced by repeated FITC-painting on the SLM. CD206+ cells after the repeated FITC-painting possessed a macrophage-like CD11b+Ly6C+ F4/80+CD64+ phenotype and expressed TIM-4, which was expressed in tolerogenic tissue-resident macrophages, at a high level. SLM CD206+ cells preferentially expressed molecules related to endocytosis and homeostatic processes, including the novel B7 family of immune checkpoint molecules, as assessed by microarray analyses. SLM CD206+ cells showed preferential expression of M2-related genes such as Fizz1, Aldh1a1 and Aldh1a2 but not Ym-1 and Arginase-1. A CD206+ cell-rich status inhibited OVA-specific CD4+ T-cell responses but reciprocally enhanced the proportion of both IL-10+CD4+ cells and Foxp3+ regulatory T-cells in regional lymph nodes. Co-culture of CD206+ cells with dendritic cells (DCs) showed that IL-12 production was suppressed in DCs concurrent with the decline of the MHC class IIhiCD86+ population, which was restored by neutralization of IL-10. These results demonstrate SLM CD206+ cells show the feature of tolerogenic macrophages and down-regulate the antigen-presenting cell function of mature DCs resulting in the inhibition of CD4+ T-cell responses.
EXpectation Propagation LOgistic REgRession on permissioned blockCHAIN (ExplorerChain): decentralized online healthcare/genomics predictive model learning
Authors: Kuo Tsung-Ting , Gabriel Rodney A , Cidambi Krishna R , Ohno-Machado Lucila 
Published: February 2020

Abstract

Objective
Predicting patient outcomes using healthcare/genomics data is an increasingly popular/important area. However, some diseases are rare and require data from multiple institutions to construct generalizable models. To address institutional data protection policies, many distributed methods keep the data locally but rely on a central server for coordination, which introduces risks such as a single point of failure. We focus on providing an alternative based on a decentralized approach. We introduce the idea using blockchain technology for this purpose, with a brief description of its own potential advantages/disadvantages.

Materials and Methods
We explain how our proposed EXpectation Propagation LOgistic REgRession on Permissioned blockCHAIN (ExplorerChain) can achieve the same results when compared to a distributed model that uses a central server on 3 healthcare/genomic datasets, and what trade-offs need to be considered when using centralized/decentralized methods. We explain how the use of blockchain technology can help decrease some of the problems encountered in decentralized methods.

Results
We showed that the discrimination power of ExplorerChain can be statistically similar to its counterpart central server-based algorithm. While ExplorerChain inherited some benefits of blockchain, it had a small increased running time.

Discussion
ExplorerChain has the same prerequisites as a distributed model with a centralized server for coordination. In a manner similar to secure multi-party computation strategies, it assumes that participating institutions are honest, but “curious.”

Conclusion
When evaluated on relatively small datasets, results suggest that ExplorerChain, which combines artificial intelligence and blockchain technologies, performs as well as a central server-based method, and may avoid some risks at the cost of efficiency.
Structure Elucidation of Urinary Metabolites of Fentanyl and Five Fentanyl Analogs using LC-QTOF-MS, Hepatocyte Incubations and Synthesized Reference Standards
Authors: Wallgren Jakob , Vikingsson Svante , Rautio Tobias , Nasr Enas , Åstrand Anna , Watanabe Shimpei , Kronstrand Robert , Gréen Henrik , Dahlén Johan , Wu Xiongyu , Konradsson Peter 
Published: February 2020

Abstract
Fentanyl analogs constitute a particularly dangerous group of new psychoactive compounds responsible for many deaths around the world. Little is known about their metabolism, and studies utilizing liquid chromatography–quadrupole time-of-flight mass spectrometry (LC–QTOF-MS) analysis of hepatocyte incubations and/or authentic urine samples do not allow for determination of the exact metabolite structures, especially when it comes to hydroxylated metabolites. In this study, seven motifs (2-, 3-, 4- and β-OH as well as 3,4-diOH, 4-OH-3-OMe and 3-OH-4-OMe) of fentanyl and five fentanyl analogs, acetylfentanyl, acrylfentanyl, cyclopropylfentanyl, isobutyrylfentanyl and 4F-isobutyrylfentanyl were synthesized. The reference standards were analyzed by LC–QTOF-MS, which enabled identification of the major metabolites formed in hepatocyte incubations of the studied fentanyls. By comparison with our previous data sets, major urinary metabolites could tentatively be identified. For all analogs, β-OH, 4-OH and 4-OH-3-OMe were identified after hepatocyte incubation. β-OH was the major hydroxylated metabolite for all studied fentanyls, except for acetylfentanyl where 4-OH was more abundant. However, the ratio 4-OH/β-OH was higher in urine samples than in hepatocyte incubations for all studied fentanyls. Also, 3-OH-4-OMe was not detected in any hepatocyte samples, indicating a clear preference for the 4-OH-3-OMe, which was also found to be more abundant in urine compared to hepatocytes. The patterns appear to be consistent across all studied fentanyls and could serve as a starting point in the development of methods and synthesis of reference standards of novel fentanyl analogs where nothing is known about the metabolism.
Screening Mammography: Guidelines versus Clinical Practice
Authors: Oudsema Rebecca , Hwang Esther , Steinberger Sharon , Yip Rowena , Margolies Laurie R 
Published: February 2020

Abstract

Objective
To understand physicians’ comprehension of breast cancer screening guidelines and the existing literature on breast cancer screening, and whether this contributes to how patient screening is implemented in clinical practice.

Methods
A survey of 18 questions was distributed across the United States via e-mail and social media resources to physicians and medical students of all disciplines and levels of training. Responses from 728 physicians and medical students were reviewed. Respondents were from over 200 different institutions and over 60 different medical specialties.

Results
Our survey demonstrates that more than half of the participants felt uncomfortable in their knowledge of breast cancer screening recommendations (399/728, 54.8%) and existing literature on breast cancer screening (555/728, 76.2%). When stratified based on level of training, those at the attending level reported a greater level of comfort in their knowledge of breast cancer screening recommendations (168/238, 70.6%) and literature (95/238, 39.9%) compared with respondents at the trainee level. Attending physicians are also more likely to recommend screening for patients between the ages of 40–49 years old (209/238, 87.7%) compared to those at the trainee level. Responses on whether to screen based on age were most consistent for patients ages 50–74, with greater than 90% of the respondents endorsing screening mammogram for this age group in all levels of training. There were greater inconsistencies in the support to screen age groups 40–49 and 75+ .

Conclusions
The results showed a disparity in screening practices by clinicians in all levels of training, particularly for patients ages 40–49 and 75+ , and for the interval of screening. Later initiation with less frequent intervals between screens may reduce the impact of screening on mortality reduction.
The Use of Dietary Antifungal Agent Terbinafine in Artificial Diet and Its Effects on Some Biological and Biochemical Parameters of the Model Organism Galleria mellonella (Lepidoptera: Pyralidae)
Authors: Kastamonuluoğlu Suzan , Büyükgüzel Kemal , Büyükgüzel Ender 
Published: February 2020

AbstractDiet quality widely affects the survival, development, fecundity, longevity, and hatchability of insects. We used the greater wax moth Galleria mellonella (Linnaeus) to determine the effects of the antifungal, antibiotic terbinafine on some of its’ biological parameters. The effects of terbinafine on malondialdehyde (MDA) and protein carbonyl (PCO) contents and the activity of the detoxification enzyme, glutathione S-transferase (GST), in the midgut of seventh-instar larvae of G. mellonella were also investigated. The insects were reared on an artificial diet containing terbinafine at concentrations of 0.001, 0.01, 0.1, and 1 g. The survival rates at all development stages of G. mellonella were significantly decreased at all terbinafine concentrations. The females from a control diet produced 82.9 ± 18.1 eggs; however, this number was significantly reduced to 51.4 ± 9.6 in females given a 0.1 g terbinafine diet. The highest concentration of terbinafine (1 g) completely inhibited egg laying. Terbinafine significantly increased MDA content and GST activity in the midgut tissue of seventh-instar larvae in a dose-dependent manner. Relative to controls, these low dietary concentrations of terbinafine significantly increased midgut PCO content; a 0.1 g terbinafine concentration raised PCO content from 155.19 ± 21.8 to 737.17 ± 36.4 nmol/mg protein. This study shows concentration-dependent effects on the biological traits of the greater wax moth G. mellonella, including the oxidative status and detoxification capacity of the midgut. Low terbinafine concentrations may be possible for use as an antifungal agent in insect-rearing diets.
Gross stomach morphology in akodontine rodents (Cricetidae: Sigmodontinae: Akodontini): a reappraisal of its significance in a phylogenetic context
Authors: Pardiñas Ulyses F J , Cañón Carola , Galliari Carlos A , Brito Jorge , Bernal Hoverud Nuria , Lessa Gisele , de Oliveira João Alves 
Published: February 2020

AbstractAkodontini, the second largest tribe within sigmodontine rodents, encompasses several stomach morphologies. This is striking because most sigmodontine groups of comparable taxonomic rank are very conservative in this respect. Based on extensive sampling of newly dissected specimens (213 stomachs representing 36 species), as well as published examples, covering almost all akodontine living genera (15 of 16), we undertook a reappraisal of the gross morphology of this organ. We then mapped this information, together with gallbladder occurrence, in a refined multilocus molecular phylogeny of the tribe. We surveyed three different configurations of stomachs in akodontines, according to the degree of development and location of the glandular epithelium; in addition, two minor variations of one of these types were described. Of the five major clades that integrate Akodontini, four are characterized by a single stomach morphology, while one clade exhibits two morphologies. Mapping stomach type on the phylogeny recovered two configurations for the most recent ancestor of Akodontini. A revised survey of gallbladder evidence also revealed overlooked congruencies. The observed stomach diversity and its arrangement in the phylogeny, along with additional morphological characters and the genetic diversity among the main clades, supports the necessity of changes in the current classification of the tribe. Recognition of subtribes or partitioning of Akodontini into several additional tribes of equal rank could be suitable options.
Ovarian and Breast Cancer Risks Associated With Pathogenic Variants in RAD51C and RAD51D
Authors: Yang Xin , Song Honglin , Leslie Goska , Engel Christoph , Hahnen Eric , Auber Bernd , Horváth Judit , Kast Karin , Niederacher Dieter , Turnbull Clare , Houlston Richard , Hanson Helen , Loveday Chey , Dolinsky Jill S , LaDuca Holly , Ramus Susan J , Menon Usha , Rosenthal Adam N , Jacobs Ian , Gayther Simon A , Dicks Ed , Nevanlinna Heli , Aittomäki Kristiina , Pelttari Liisa M , Ehrencrona Hans , Borg Åke , Kvist Anders , Rivera Barbara , Hansen Thomas V O , Djursby Malene , Lee Andrew , Dennis Joe , Bowtell David D , Traficante Nadia , Diez Orland , Balmaña Judith , Gruber Stephen B , Chenevix-Trench Georgia , Investigators kConFab , Jensen Allan , Kjær Susanne K , Høgdall Estrid , Castéra Laurent , Garber Judy , Janavicius Ramunas , Osorio Ana , Golmard Lisa , Vega Ana , Couch Fergus J , Robson Mark , Gronwald Jacek , Domchek Susan M , Culver Julie O , de la Hoya Miguel , Easton Douglas F , Foulkes William D , Tischkowitz Marc , Meindl Alfons , Schmutzler Rita K , Pharoah Paul D P , Antoniou Antonis C 
Published: February 2020

Abstract

Background
The purpose of this study was to estimate precise age-specific tubo-ovarian carcinoma (TOC) and breast cancer (BC) risks for carriers of pathogenic variants in RAD51C and RAD51D.

Methods
We analyzed data from 6178 families, 125 with pathogenic variants in RAD51C, and 6690 families, 60 with pathogenic variants in RAD51D. TOC and BC relative and cumulative risks were estimated using complex segregation analysis to model the cancer inheritance patterns in families while adjusting for the mode of ascertainment of each family. All statistical tests were two-sided.

Results
Pathogenic variants in both RAD51C and RAD51D were associated with TOC (RAD51C: relative risk [RR] = 7.55, 95% confidence interval [CI] = 5.60 to 10.19; P = 5 × 10-40; RAD51D: RR = 7.60, 95% CI = 5.61 to 10.30; P = 5 × 10-39) and BC (RAD51C: RR = 1.99, 95% CI = 1.39 to 2.85; P = 1.55 × 10-4; RAD51D: RR = 1.83, 95% CI = 1.24 to 2.72; P = .002). For both RAD51C and RAD51D, there was a suggestion that the TOC relative risks increased with age until around age 60 years and decreased thereafter. The estimated cumulative risks of developing TOC to age 80 years were 11% (95% CI = 6% to 21%) for RAD51C and 13% (95% CI = 7% to 23%) for RAD51D pathogenic variant carriers. The estimated cumulative risks of developing BC to 80 years were 21% (95% CI = 15% to 29%) for RAD51C and 20% (95% CI = 14% to 28%) for RAD51D pathogenic variant carriers. Both TOC and BC risks for RAD51C and RAD51D pathogenic variant carriers varied by cancer family history and could be as high as 32–36% for TOC, for carriers with two first-degree relatives diagnosed with TOC, or 44–46% for BC, for carriers with two first-degree relatives diagnosed with BC.

Conclusions
These estimates will facilitate the genetic counseling of RAD51C and RAD51D pathogenic variant carriers and justify the incorporation of RAD51C and RAD51D into cancer risk prediction models.
Definitive chemoradiotherapy for squamous cell carcinoma of the esophagus: outcomes for borderline-resectable disease
Authors: Ishikura Satoshi , Kondo Takuhito , Murai Taro , Ozawa Yoshiyuki , Yanagi Takeshi , Sugie Chikao , Miyakawa Akifumi , Shibamoto Yuta 
Published: February 2020

Abstract
Definitive chemoradiotherapy (dCRT) is the standard treatment for unresectable esophageal cancer. Induction chemotherapy has been actively investigated for borderline-resectable and unresectable disease, but the superiority over dCRT has yet to be confirmed. The purpose of this study was to evaluate the outcome of dCRT with special interest in borderline-resectable disease. Patients with esophageal cancer treated with dCRT between January 2004 and November 2016 were included in this retrospective analysis. Chemotherapy consisted of two cycles of cisplatin (70–75 mg/m2) on day 1 and 5-fluorouracil (700–1000 mg/m2 per day) on days 1–4 or low-dose cisplatin (10 mg/m2 per day) and 5-fluorouracil (175 mg/m2 per day) for 20 days. Radiotherapy was given with a daily fraction of 1.8–2 Gy to a total dose of 50–70 Gy. A total of 104 patients were included: 34 were resectable, 35 were borderline-resectable and 35 were unresectable. Complete response was achieved in 44 patients (42%). Eighteen patients (17%) suffered Grade 2 or greater cardiopulmonary toxicity and seven patients (7%) suffered Grade 3 cardiopulmonary toxicity. At the time of this analysis, 59 patients were dead and 45 were censored. The 3-year overall survival proportions for resectable, borderline-resectable and unresectable patients were 64%, 46% and 21%, respectively. The overall survival for borderline-resectable patients with complete response and noncomplete response was significantly different (P &lt; 0.001), with 3-year survival of 70% and 8%, respectively. The overall survival for complete response patients with borderline-resectable disease was encouraging. Further investigation to find a subgroup fit for esophagus-preserving treatment is warranted.
Draparnaldia: a chlorophyte model for comparative analyses of plant terrestrialization
Authors: Caisová Lenka 
Published: February 2020

AbstractIt is generally accepted that land plants evolved from streptophyte algae. However, there are also many chlorophytes (a sister group of streptophyte algae and land plants) that moved to terrestrial habitats and even resemble mosses. This raises the question of why no land plants evolved from chlorophytes. In order to better understand what enabled streptophyte algae to conquer the land, it is necessary to study the chlorophytes as well. This review will introduce the freshwater filamentous chlorophyte alga Draparnaldia sp. (Chaetophorales, Chlorophyceae) as a model for comparative analyses between these two lineages. It will also focus on current knowledge about the evolution of morphological complexity in chlorophytes versus streptophytes and their respective morphological/behavioural adaptations to semi-terrestrial habitats, and will show why Draparnaldia is needed as a new model system.
Say it with double flowers
Authors: Abdirashid Hashim , Lenhard Michael 
Published: February 2020

This article comments on:Gattolin, S, Cirilli M, Chessa S, et al. 2020. Mutations in orthologous PETALOSA TOE-type genes cause dominant double-flower phenotype in phylogenetically distant eudicots. Journal of Experimental Botany 71, 2585–2595.
Check the grammar of your translation: The usefulness of WhiteSmoke as an automated feedback program
Authors: Etemad Amir Reza Nemat Tabrizi and Parisa 
Published: February 2020

AbstractThe use of technology in teaching and learning a second language has been an increasingly important subject of research recently. Various software and applications have been developed to aid the students to identify and correct their grammatical mistakes. The present study aimed to assess the effect of an automated feedback program, WhiteSmoke, on the accuracy of the translated texts by Iranian translation students. To pursue the purpose of the study, 68 male and female students studying at Payame Noor University, Tabriz-Iran were selected among 106 undergraduate students of English translation, based on their performance on Nelson proficiency test and a translation accuracy test. The participants shaped the experimental group and the control group of the study. The experimental group included twenty-six trainees, while the control group included forty-two trainees. They were required to translate a Persian text into English as pretest to homogenize them based on their translation accuracy. After 8 weeks of treatment, posttest was administered to the participants of both groups. The results indicated that translation trainees receiving automated written corrective feedback through WhiteSmoke improved their ability in translation in terms of accuracy. The result might have implications for translation trainers, language teachers, learners, and materials developers.