bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of putative circular plasmids in sponge‐associated bacterial communities using a selective multiply‐primed rolling circle amplification
Authors: Oliveira Vanessa , Polónia Ana R. M. , Cleary Daniel F. R. , Huang Yusheng M. , de Voogd Nicole J. , da Rocha Ulisses N. , Gomes Newton C. M. 
Published: August 2020

AbstractPlasmid transfers among bacterial populations can directly influence the ecological adaptation of these populations and their interactions with host species and environment. In this study, we developed a selective multiply‐primed rolling circle amplification (smRCA) approach to enrich and characterize circular plasmid DNA from sponge microbial symbionts via high‐throughput sequencing (HTS). DNA (plasmid and total community DNA) obtained from sponge (Cinachyrella sp.) samples and a bacterial symbiont (Vibrio sp. CyArs1) isolated from the same sponge species (carrying unknown plasmids) were used to develop and validate our methodology. The smRCA was performed during 16 hr with 141 plasmid‐specific primers covering all known circular plasmid groups. The amplified products were purified and subjected to a reamplification with random hexamer primers (2 hr) and then sequenced using Illumina MiSeq. The developed method resulted in the successful amplification and characterization of the sponge plasmidome and allowed us to detect plasmids associated with the bacterial symbiont Vibrio sp. CyArs1 in the sponge host. In addition to this, a large number of small (<2 kbp) and cryptic plasmids were also amplified in sponge samples. Functional analysis identified proteins involved in the control of plasmid partitioning, maintenance and replication. However, most plasmids contained unknown genes, which could potentially serve as a resource of unknown genetic information and novel replication systems. Overall, our results indicate that the smRCA‐HTS approach developed here was able to selectively enrich and characterize plasmids from bacterial isolates and sponge host microbial communities, including plasmids larger than 20 kbp.
Using intrinsic and contextual information associated with automated signal detections to improve call recognizer performance: A case study using the cryptic and critically endangered Night Parrot Pezoporus occidentalis
Authors: Leseberg Nicholas P. , Venables William N. , Murphy Stephen A. , Watson James E. M. 
Published: August 2020

Abstract

Rapid expansion in the collection of large acoustic datasets to answer ecological questions has generated a parallel requirement for techniques that streamline analysis of these datasets. In many cases, automated signal recognition algorithms, often termed ‘call recognizers’, are the only feasible option for doing this. To date, most research has focused on what types of recognizers perform best, and how to train these recognizers to optimize performance.

We demonstrate that once recognizer construction is complete and the data processed, further improvements are possible using intrinsic and contextual information associated with each detection. We initially construct a call recognizer for the Night Parrot Pezoporus occidentalis using the r package monitoR, and scan a test dataset. We then examine a number of intrinsic variables associated with each detection generated by the recognizer, and several contextual variables associated with the species' environment and ecology, to determine if they might help predict whether a given detection is a true positive (target signal) or false positive (non‐target signal). We test several logistic regression models incorporating different combinations of intrinsic and contextual variables, selecting the best‐performing model for application. We train the model, using it to calculate the probability each detection is a true or false positive.

Substituting this model‐derived probability for raw recognizer score improved the recognizer's performance, reducing the number of detections requiring proofing by 60% to achieve a recall of 90%, and by 76% to achieve a recall of 75%.

This technique is applicable to any recognizer output, regardless of the underlying algorithm. Application requires an understanding of how the recognizer algorithm determines matches, and knowledge of a species' ecology and environment. Because advanced programming skills and expertise are not required to apply this technique, it will be particularly relevant to field ecologists for whom building and operating call recognizers is an element of their research toolbox, but not necessarily a focus.
colorist: An r package for colouring wildlife distributions in space–time
Authors: Schuetz Justin G. , Strimas‐Mackey Matthew , Auer Tom 
Published: August 2020

Abstract

Maps are essential tools for communicating information about wildlife distributions in space and time. As observational datasets grow and enable description of distributions at broader spatiotemporal extents and finer spatiotemporal resolutions, new opportunities arise for visualizing when and where animals occur.

Here we present a package for the r statistical computing environment, colorist, that facilitates visualization of animal distributions in space and time using raster inputs. In addition to enabling display of sequential change in distributions through the use of small multiples, colorist provides functions for extracting several features of interest from a sequence of distributions and for visualizing those features within an HCL (hue–chroma–luminance) colour space.

Resulting maps allow for ‘fair’ visual comparison of occurrence, abundance or probability density values across space and time and can be used to address questions about where, when and how consistently a species or individual is likely to be found. Functions can also be harnessed to visualize distributions of multiple species or individuals within a single time period when research questions are focused on understanding the degree to which species or individuals partition space.

By colouring temporal features of distributions, while simultaneously controlling their perceptual weight, we expand the set of tools available for exploring wildlife movements through space–time and for communicating research results. We expect colorist functions will prove useful for visualizing other types of multivariate data that we have yet to consider.
High Alcohol–Preferring Mice Show Reaction to Loss of Ethanol Reward Following Repeated Binge Drinking
Authors: Ardinger Cherish E. , Grahame Nicholas J. , Lapish Christopher C. , Linsenbardt David N. 
Published: August 2020

BackgroundBeyond yielding high blood ethanol (EtOH) concentrations (BECs), binge‐drinking models allow examination of drinking patterns which may be associated with EtOH’s rewarding effects, including front‐loading and consummatory successive negative contrast (cSNC), a decrease in intake when only water is available to subjects expecting EtOH. The goals of the current study were to broaden our understanding of these reward‐related behaviors during binge EtOH access in high alcohol–preferring (HAP) replicate lines (HAP2 and HAP3) of mice selectively bred to prefer alcohol. We hypothesized that both lines would show evidence of front‐loading during binge EtOH access and that we would find a cSNC effect in groups where EtOH was replaced with water, as these results have been shown previously in HAP1 mice.MethodsHAP replicate 2 and replicate 3 female and male mice were given 2 hours of EtOH or water access in the home cage for 15 consecutive days using "drinking in the dark" (DID) procedures. Mice received the same fluid (either 20% unsweetened EtOH or water) for the first 14 days. However, on the 15th day, half of the mice from these 2 groups were provided with the opposite assigned fluid (EtOH groups received water and vice versa). Intake was measured in 1‐minute bins using specialized sipper tubes, which allowed within‐session analyses of binge‐drinking patterns.ResultsEtOH front‐loading was observed in both replicates. HAP3 mice displayed front‐loading on the first day of EtOH access, whereas front‐loading developed following alcohol experience in HAP2 mice, which may suggest differences in initial sensitivity to EtOH reward. Consummatory SNC, which manifests as lower water intake in mice expecting EtOH as compared to mice expecting water, was observed in both replicates.ConclusionsThese findings increase confidence that defined changes in home cage consummatory behavior are driven by the incentive value of EtOH. The presence of cSNC across HAP replicates indicates that this reaction to loss of reward is genetically mediated, which suggests that there is a biological mechanism that might be targeted.
Association of frequency of perceived exposure to discrimination with tobacco withdrawal symptoms and smoking lapse behavior in African Americans
Authors: Bello Mariel S. , Liautaud Madalyn M. , De La Cerda Julianne T. , Pang Raina D. , Ray Lara A. , Ahluwalia Jasjit A. , Leventhal Adam M. 
Published: August 2020

AbstractBackground and AimsFrequent experiences of discrimination could increase vulnerability to tobacco withdrawal and smoking lapse in populations subject to tobacco‐related health disparities. This laboratory study (2013–17) examined whether individual differences in perceived exposure to discrimination in one's daily life predicted tobacco withdrawal symptoms and smoking lapse behavior following acute tobacco deprivation in African American smokers.DesignMixed design with the between‐subjects continuous variable of perceived discrimination crossed with the within‐subject variable of tobacco deprivation status (deprived versus non‐deprived).SettingAcademic medical center in Los Angeles, CA, USA.ParticipantsAfrican American non‐treatment seeking daily cigarette smokers (n = 607, ≥ 10 cig/day).MeasurementsAt a baseline visit, self‐reported frequency of perceived exposure to discrimination in one's daily life was measured [everyday discrimination scale (EDDS)]. At two subsequent counterbalanced experimental visits (16‐hour tobacco deprivation versus ad‐libitum smoking), self‐report assessments of various tobacco withdrawal symptom domains [Brief Questionnaire of Smoking Urges), Wisconsin Smoking Withdrawal Scale (WSWS), Profile of Mood States (POMS), Snaith–Hamilton Pleasure Scale (SHAPS) and Current Impulsivity Scale (CIS)) and a behavioral smoking lapse analogue task were measured.FindingsAdjusted models demonstrated that greater frequency of perceived exposure to discrimination was associated with larger deprivation‐induced increases in acute urges to smoke to alleviate negative mood, several negative mood states and subjective cognitive functioning—effect sizes were small in magnitude (βs = 0.09–0.13; Ps < 0.02). Data were inconclusive for associations between perceived exposure to discrimination and deprivation‐induced changes in cravings, urges to smoke for pleasure, positive mood reduction, other symptoms or smoking reinstatement behavior.ConclusionsFrequency of perceived exposure to discrimination appears to be modestly associated with increased severity of some deprivation‐induced tobacco withdrawal symptoms in African American smokers.
Mechanical circulatory support for early surgical repair of postinfarction ventricular septal defect with cardiogenic shock
Authors: Vondran Maximilian , Wehbe Mahmoud S. , Etz Christian , Ghazy Tamer , Rastan Ardawan J. , Borger Michael A. , Schroeter Thomas 
Published: August 2020

AbstractPostinfarction ventricular septal defect (pVSD) due to acute myocardial infarction complicated by cardiogenic shock (CS) is associated with high mortality. The aim of this study was to determine the outcome of primary surgical repair of pVSD in patients with CS and examine whether it is influenced by the use of mechanical circulatory support (MCS) devices. Between October 1994 and April 2016, primary surgical repair of pVSD complicated by CS was performed in 53 patients. Thirty‐six (68%) were implanted pre‐operatively with an intra‐aortic balloon pump (IABP), 4 (8%) with extracorporeal life support (ECLS), and 13 (24%) received no MCS device. Prospectively collected demographic and perioperative data were analyzed retrospectively. All‐cause, 30‐day mortality rates were analyzed and multivariate analysis was performed to differentiate independent risk factors. No pre‐operatively implanted MCS device was able to improve 30‐day survival, whereas pre‐operatively implanted ECLS tended to have a positive effect (P = .106). The post‐operative need for a MCS device or escalation of MCS invasiveness (IABP upgrade to ECLS) was associated with a higher 30‐day mortality (P = .001) compared with patients without any MCS device or those with pre‐operatively implanted MCS devices. An independent risk factor for 30‐day mortality was the interval between acute myocardial infarction and surgery <7 days (OR 5.895, CI 1.615‐21.515; P = .007). Pre‐operative implantation of ECLS for CS tends to improve the outcome of early primary surgical pVSD repair. The need for a post‐operative MCS device is associated with a worse 30‐day survival after early primary surgical pVSD repair.
Pharmacogenetic studies of thiopurine methyltransferase genotype‐phenotype concordance and effect of methotrexate on thiopurine metabolism
Authors: Zimdahl Kahlin Anna , Helander Sara , Wennerstrand Patricia , Vikingsson Svante , Mårtensson Lars‐Göran , Appell Malin Lindqvist 
Published: August 2020

AbstractThe discovery and implementation of thiopurine methyltransferase (TPMT) pharmacogenetics has been a success story and has reduced the suffering from serious adverse reactions during thiopurine treatment of childhood leukaemia and inflammatory bowel disease. This MiniReview summarizes four studies included in Dr Zimdahl Kahlin's doctoral thesis as well as the current knowledge on this field of research. The genotype‐phenotype concordance of TPMT in a cohort of 12 663 individuals with clinically analysed TPMT status is described. Notwithstanding the high concordance, the benefits of combined genotyping and phenotyping for TPMT status determination are discussed. The results from the large cohort also demonstrate that the factors of gender and age affect TPMT enzyme activity. In addition, characterization of four previously undescribed TPMT alleles (TPMT*41, TPMT*42, TPMT*43 and TPMT*44) shows that a defective TPMT enzyme could be caused by several different mechanisms. Moreover, the folate analogue methotrexate (MTX), used in combination with thiopurines during maintenance therapy of childhood leukaemia, affects the metabolism of thiopurines and interacts with TPMT, not only by binding and inhibiting the enzyme activity but also by regulation of its gene expression.
Disordered serum erythroferrone and hepcidin levels as indicators of the spontaneous abortion occurrence during early pregnancy in humans
Authors: Wei Shuting , Liu Wei , Qi Yu , Guo Yifan , Zhang Shuping , Wang Li , Zhuang Taifeng , Zhang Na , Liu Sijin 
Published: August 2020

SummarySpontaneous abortion is a common, detrimental outcome of pregnancy, and can be induced by a variety of factors, including pathophysiological conditions and socioeconomic circumstances. Despite numerous studies examining the aetiology of spontaneous abortion, there is limited understanding of the disordered iron transportation between mother and fetus through the placenta. Recently, erythroferrone (ERFE) was recognized as a novel negative regulator of hepcidin that can elevate nutritional iron absorption and macrophagic iron egress for enhanced erythropoiesis. However, its diagnostic significance in different disease conditions associated with iron remains poorly understood. In the current study, we discovered disordered maternal iron homeostasis in women who had spontaneous abortions during early pregnancy, as characterized by increased serum iron and hepcidin levels, and conversely, reduced serum ERFE levels, compared to healthy control individuals and women with normal pregnancy. Comprehensive statistical analyses revealed the correlation between different variables and pregnancy status, signifying the pronounced diagnostic value of an increased ratio of serum hepcidin and ERFE (HE ratio) in recognizing adverse pregnancy status. In contrast to previous non‐selective discrete surrogates, such as iron, hepcidin and ferritin, the HE ratio may otherwise stand for a novel and more representative hallmark for early spontaneous abortion.
Short somatic alterations at the site of copy number variation in breast cancer
Authors: Murakami Fumi , Tsuboi Yumi , Takahashi Yuka , Horimoto Yoshiya , Mogushi Kaoru , Ito Takeshi , Emi Mitsuru , Matsubara Daisuke , Shibata Tatsuhiro , Saito Mitsue , Murakami Yoshinori 
Published: August 2020

AbstractCopy number variation (CNV) is a polymorphism in the human genome involving DNA fragments larger than 1 kb. Copy number variation sites provide hotspots of somatic alterations in cancers. Herein, we examined somatic alterations at sites of CNV in DNA from 20 invasive breast cancers using a Comparative Genomic Hybridization array specifically designed to detect the genome‐wide CNV status of approximately 412 000 sites. Somatic copy number alterations (CNAs) were detected in 39.9% of the CNV probes examined. The most frequently altered regions were gains of 1q21‐22 (90%), 8q21‐24 (85%), 1q44 (85%), and 3q11 (85%) or losses of 16q22‐24 (80%). Gene ontology analyses of genes within the CNA fragments revealed that cascades related to transcription and RNA metabolism correlated significantly with human epidermal growth factor receptor 2 positivity and menopausal status. Thirteen of 20 tumors showed CNAs in more than 35% of sites examined and a high prevalence of CNAs correlated significantly with estrogen receptor (ER) negativity, higher nuclear grade (NG), and higher Ki‐67 labeling index. Finally, when CNA fragments were categorized according to their size, CNAs smaller than 10 kb correlated significantly with ER positivity and lower NG, whereas CNAs exceeding 10 Mb correlated with higher NG, ER negativity, and a higher Ki‐67 labeling index. Most of these findings were confirmed or supported by quantitative PCR of representative DNA fragments in 72 additional breast cancers. These results suggest that most CNAs are caused by gain or loss of large chromosomal fragments and correlate with NG and several malignant features, whereas solitary CNAs of less than 10 kb could be involved in ER‐positive breast carcinogenesis.
Olfactory changes after endoscopic sinus surgery for chronic rhinosinusitis: A meta‐analysis
Authors: Zhao Rui , Chen Kai , Tang Yuedi 
Published: August 2020

AbstractBackgroundEndoscopic sinus surgery (ESS) is an important treatment modality for chronic rhinosinusitis (CRS). However, its effect on olfaction remains controversial.Objective of reviewTo assess the olfactory impact of ESS in patients with CRS.Type of reviewA meta‐analysis.Search strategyA systematic literature search in the PubMed, EMBASE and Cochrane Library databases was conducted to identify studies that assessed change in olfaction after ESS in patients with CRS. Search terms were related to paranasal sinus diseases, smell and endoscopy.Evaluation methodThe extracted data included authors, publication year, study type, age, sex, diagnostic criteria, surgical mode, sample size, follow‐up time, olfaction measurement tool and outcome. We analysed the olfactory changes as continuous variables.ResultsThirty‐five studies including 3164 patients with CRS were eligible for the meta‐analysis. Among patients having CRS with nasal polyps, olfactory dysfunction improved, as assessed by the Sniffin' Sticks total score (P = .000), Sniffin' Sticks discrimination score (P = .023), Sniffin' Sticks identification score (P = .005), University of Pennsylvania Smell Identification Test (P = .046) and Visual Analogue Scale (P = .000). However, the threshold score of the Sniffin' Sticks test did not improve significantly (P = .361). Olfactory dysfunction did not improve in patients having CRS without nasal polyps according to the University of Pennsylvania Smell Identification Test (P = .404). In non‐classified CRS patients, improvement in olfactory dysfunction was observed according to the University of Pennsylvania Smell Identification Test (P = .000), Visual Analogue Scale (P = .001) and Questionnaire of Olfactory Disorders‐Negative Statements (P = .001). However, there were no significant improvements according to the Brief Smell Identification Test (P = .325), Sniffin' Sticks threshold score (P = .160) and Sniffin' Sticks identification score (P = .079).ConclusionEndoscopic sinus surgery may be beneficial for improvement in olfactory conditions in patients with CRS. Further thorough and comprehensive studies need to be conducted.
Ultrathin colonoscopy can improve complete preoperative colonoscopy for stenotic colorectal cancer: Prospective observational study
Authors: Ito Sayo , Hotta Kinichi , Imai Kenichiro , Kishida Yoshihiro , Takizawa Kohei , Kakushima Naomi , Kawata Noboru , Yoshida Masao , Yabuuchi Yohei , Ishiwatari Hirotoshi , Matsubayashi Hiroyuki , Shiomi Akio , Ono Hiroyuki 
Published: August 2020

ObjectivesPreoperative colonoscopy is often incomplete for stenotic colorectal cancers (CRC). This prospective observational study aimed to evaluate the ability of an ultrathin colonoscope (UTC) to inspect the whole colon by passing through the stenotic CRC.MethodsAll patients who underwent preoperative colonoscopy for stenotic CRCs at Shizuoka Cancer Center were examined for eligibility. If a standard colonoscope (PCF‐H290ZI) could not pass because of a stenosis, the patients were recruited. All of the eligible patients were prospectively enrolled when informed consent could be obtained, and complete colonoscopy was attempted again using an UTC (PCF‐PQ260L). Patients with stent placement and those requiring right hemicolectomy were not recruited. Primary endpoints were pass‐through and cecal intubation rates. The detected synchronous neoplasias (adenomas and cancers) and their pathological findings after resection were evaluated.ResultsA total of 100 patients were enrolled between September 2017 and February 2019. The mean age was 65.6 ± 10.8 years, and 59% were male. The pass‐through and cecal intubation rates were 67% (67/100) and 58% (58/100), respectively. Synchronous lesions located proximal to the stenoses were detected in 65.5% (38/58) of the complete colonoscopies, with a total of 86 lesions, including 18 advanced neoplasias with three invasive cancers.ConclusionWhen standard colonoscopy cannot pass through stenotic CRC, ultrathin colonoscopy can be considered as an option to inspect the whole colon proximal to the stenosis because treatment strategy can potentially be changed by detecting synchronous neoplasias proximal to the stenosis before surgery. (UMIN000028505)
The relation between municipal and government bond yields in an era of unconventional monetary policy
Authors: Knezevic David , Nordström Martin , Österholm Pär 
Published: August 2020

AbstractIn this paper, we investigate how the 5‐year Swedish municipal bond yield has been related to the corresponding yield on government bonds during the period that the Riksbank has conducted unconventional monetary policy in terms of bond purchases. Using daily Swedish data on bond yields from February 2015 to January 2018, we first conduct an event study to assess the short‐run effects of the Riksbank's bond‐purchase announcements. We then estimate bivariate vector autoregressive models to study the dynamic relationship between the yields. Results from the event study suggest that the accumulated short‐run effect of the Riksbank's announcements was to lower the government bond yield by approximately 40 to 50 basis points and municipal bond yields by 30 to 35 basis points. Our vector autoregressive analysis indicates—in line with the event study—that an unexpected decrease in the government bond yield initially increases the municipal bond‐yield spread. However, after approximately 4 weeks, the effect has been reversed and the municipal bond‐yield spread is lower than it was initially. By conducting this analysis, we contribute to the understanding of the transmission of unconventional monetary policy.