bluuebunny/crossref_metadata_2025_split huggingface dataset:
Which patients with acute myeloid leukemia in CR1 can be spared an allogeneic transplant?
Authors: Craddock Charles , Raghavan Manoj 
Published: January 2019

Purpose of review
Disease relapse remains the major cause of treatment failure in adults with acute myeloid leukemia (AML) in first complete remission (CR1) treated with intensive chemotherapy alone. Allogeneic stem cell transplantation (allo-SCT) reduces the risk of disease recurrence, and thus the advent of reduced intensity-conditioning regimens coupled with increased donor availability has increased the deliverability of potentially curative transplant therapy in AML. However, allo-SCT remains associated with significant additional morbidity and mortality, and it is therefore important to identify patients whose outcome if treated with chemotherapy alone is good enough to spare them the risks associated with allo-SCT.

Recent findings
Characterization of cytogenetic and molecular abnormalities present at diagnosis coupled with dynamic assessments of measurable residual disease now permit greater accuracy in defining the relapse risk in patients treated with chemotherapy alone. At the same time, the risk of transplant-related mortality can be predicted by a number of scoring systems which assess patient comorbidity. Taken together, such assessments permit a dynamic assessment of the risks and benefits of transplantation aiding the identification of patients who are unlikely to benefit from transplantation in CR1.

Summary
Increasingly accurate risk stratification in adults with AML CR1 aids the rational utilization of allo-SCT. Future research integrating the results of serial MRD analysis in molecularly defined subtypes of AML will further improve rational selection of patients for transplant.
Prevalence and Outcome of HIV-associated Malignancies Among HIV-infected Children Enrolled into Care at Kilimanjaro Christian Medical Center 2006 to 2014: A Hospital-based Retrospective Analytical Study
Authors: Irira Michael , Ngocho James S. , Youze Joshua , Shayo Irene , Komba Venancia , Minja Linda , Karia Francis P. , Bartlett John , Mmbaga Blandina T. 
Published: January 2019

Objective:
We aimed to establish the prevalence of human immunodeficiency virus (HIV)-associated malignancies in children attending a care and treatment clinic at Kilimanjaro Christian Medical Centre.

Materials and Methods:
This was a retrospective cross-sectional hospital-based study of children who attended an HIV care and treatment clinic between 2006 and 2014. Children 2 months to 17 years of age were eligible for participation. The data on social demographic and clinical characteristics were extracted from the medical record. A multivariate logistic regression model was developed to determine predictors of HIV-associated malignancies.

Results:
Medical records from 721 HIV-infected children were reviewed. The median age (interquartile range) at HIV diagnosis was 5.7 (2.0 to 9.4) years. Among them, 34 (4.7%) had HIV-associated malignancies. The most common (n=24, 70.3%) malignancy was the Kaposi sarcoma. Age at HIV diagnosis was significantly associated with HIV-associated malignancies (adjusted odds ratio, 1.2; 95% confidence interval, 1.0-1.3). Among 34 patients with HIV-associated malignancies, 11 (32.4%) died. Seven (20.6%) patients reported complete remission from their malignancies, and outcomes for 6 patients were unknown.

Conclusions:
The prevalence of HIV-associated malignancies was high and was associated with late HIV diagnosis. The Kaposi sarcoma was the commonest malignancy. Early HIV diagnosis and treatment in children might reduce HIV-associated malignancies.
Generating real-world tumor burden endpoints from electronic health record data: Comparison of RECIST, radiology-anchored, and clinician-anchored approaches for abstracting real-world progression in non-small cell lung cancer
Authors: Griffith Sandra D. , Tucker Melisa , Bowser Bryan , Calkins Geoffrey , Chang Che-hsu (Joe) , Guardino Ellie , Khozin Sean , Kraut Josh , Miksad Rebecca , You Paul , Schrag Deb , Abernethy Amy P. 
Published: January 2019

AbstractReal-world evidence derived from electronic health records (EHRs) is increasingly recognized as a supplement to evidence generated from traditional clinical trials. In oncology, tumor-based Response Evaluation Criteria in Solid Tumors (RECIST) endpoints are collected in clinical trials. The best approach for collecting similar endpoints from EHRs remains unknown. We evaluated the feasibility of a traditional RECIST-based methodology to assess EHR-derived real-world progression (rwP) and explored non-RECIST-based approaches. In this retrospective study, cohorts were randomly selected from Flatiron Health’s database of patient-level EHR data in advanced non-small cell lung cancer. A RECIST-based approach was tested for feasibility (N=26). Three non-RECIST abstraction approaches were tested for feasibility, reliability, and validity (N=200): (1) radiology-anchored, (2) clinician-anchored, and (3) combined. RECIST-based cancer progression could be ascertained from the EHRs of 23% of patients (6/26). In 87% of patients (173/200), at least one rwP event was identified using both the radiology- and clinician-anchored approaches. rwP dates matched 90% of the time. In 72% of patients (124/173), the first clinician-anchored rwP event was accompanied by a downstream event (e.g., treatment change); the association was slightly lower for the radiology-anchored approach (67%; 121/180). Median overall survival (OS) was 17 months (95% confidence interval [CI]: 14, 19). Median real-world progression-free survival (rwPFS) was 5.5 (95% CI: 4.6, 6.3) and 4.9 months (95% CI: 4.2, 5.6) for clinician-anchored and radiology-anchored approaches, respectively. Correlations between rwPFS and OS were similar across approaches (Spearman’s rho: 0.65-0.66). Abstractors preferred the clinician-anchored approach as it provided more comprehensive context. RECIST cannot adequately assess cancer progression in EHR-derived data due to missing data and lack of clarity in radiology reports. We found a clinician-anchored approach supported by radiology report data to be the optimal, and most practical, method for characterizing tumor-based endpoints from EHR-sourced data.
Professional Swimmers and Normal Populations have Different Patterns of Epidermal Green Autofluorescence
Authors: Tao Yue , Zhang Mingchao , Li Yujia , Shen Xunzhang , Ying Weihai 
Published: January 2019

AbstractOur recent studies have suggested that green autofluorescence of the fingernails and certain regions of skin may be novel biomarkers for disease diagnosis and evaluation of the injury state of cardiovascular system. Our study has also suggested that oxidative stress may produce the increased epidermal green AF by altering keratin 1. Since athletes’ body may have increased oxidative stress and inflammation, we proposed our hypothesis that athletes may have increased green AF in their fingernails and certain regions of their skin. In current study we tested this hypothesis by determining the green AF of professional swimmers. We found that compared with age-matched controls, both the green AF intensity and AF asymmetry in both right and left antebrachium and Ventriantebrachium of the professional swimmers is significantly higher. In left Dorsal Centremetacarpus, the green AF intensity of the professional swimmers is significantly higher than that of the age-matched controls. In contrast, the green AF intensity or AF asymmetry of the professional swimmers is not significantly different from that of the age-matched controls in Centremetacarpus, Ventroforefinger, Dorsal Index Finger and Index Fingernails. Collectively, our study has provided first evidence suggesting that athletes have increased green AF intensity and asymmetry in certain regions of their skin. Based on this finding, we may evaluate non-invasively the levels of oxidative damage and inflammation in athletes’ body.
Using Twitter To Generate Signals For The Enhancement Of Syndromic Surveillance Systems: Semi-Supervised Classification For Relevance Filtering in Syndromic Surveillance
Authors: Edo-Osagie Oduwa , Smith Gillian , Lake Iain , Edeghere Obaghe , De La Iglesia Beatriz 
Published: January 2019

AbstractWe investigate the use of Twitter data to deliver signals for syndromic surveillance in order to assess its ability to augment existing syndromic surveillance efforts and give a better understanding of symptomatic people who do not seek health care advice directly. We focus on a specific syndrome - asthma/difficulty breathing. We outline data collection using the Twitter streaming API as well as analysis and pre-processing of the collected data. Even with keyword-based data collection, many of the tweets collected are not be relevant because they represent chatter, or talk of awareness instead of suffering a particular condition. In light of this, we set out to identify relevant tweets to collect a strong and reliable signal. For this, we investigate text classification techniques, and in particular we focus on semi-supervised classification techniques since they enable us to use more of the Twitter data collected without needing to label it all. In this paper, propose a semi-supervised approach to symptomatic tweet classification and relevance filtering. We also propose the use of emojis and other special features capturing the tweet’s tone to improve the classification performance. Our results show that negative emojis and those that denote laughter provide the best classification performance in conjunction with a simple bag of words approach. We obtain good performance on classifying symptomatic tweets with both supervised and semi-supervised algorithms and found that the proposed semi-supervised algorithms preserve more of the relevant tweets and may be advantegeous in the context of a weak signal. Finally, we found some correlation (r = 0.414, p = 0.0004) between the Twitter signal generated with the semi-supervised system and data from consultations for related health conditions.
RUNX1 mitotically bookmarks target genes that are important for the mammary epithelial-to-mesenchymal transition
Authors: Rose Joshua T. , Moskovitz Eliana , Boyd Joseph R. , Gordon Jonathan A. , Bouffard Nicole A. , Fritz Andrew J. , Illendula Anuradha , Bushweller John H. , Lian Jane B. , Stein Janet L. , Stein Gary S. , Zaidi Sayyed K. 
Published: January 2019

ABSTRACTRUNX1 has recently been shown to play an important role in determination of mammary epithelial cell identity. However, mechanisms by which loss of the RUNX1 transcription factor in mammary epithelial cells leads to epithelial-to-mesenchymal transition (EMT) are not known. Here, we report mitotic bookmarking of genes by RUNX1 as a potential mechanism to convey regulatory information through successive cell divisions for coordinate control of mammary cell proliferation, growth, and identity. Genome-wide RUNX1 occupancy profiles for asynchronous, mitotically enriched, and early G1 breast epithelial cells reveal RUNX1 is retained during the mitosis to G1 transition on protein coding and long non-coding RNA genes critical for mammary epithelial proliferation, growth, and phenotype maintenance. Disruption of RUNX1 DNA binding and association with mitotic chromosomes alters cell morphology, global protein synthesis, and phenotype-related gene expression. Together, these findings show for the first time that RUNX1 bookmarks a subset of epithelial-related genes during mitosis that remain occupied as cells enter the next cell cycle. Compromising RUNX1 DNA binding initiates EMT, an essential first step in the onset of breast cancer.SignificanceThis study elucidates mitotic gene bookmarking as a potential epigenetic mechanism that impacts breast epithelial cell growth and phenotype and has potential implications in breast cancer onset.
YeasTSS: An Integrative Web Database of Yeast Transcription Start Sites
Authors: McMillan Jonathan , Lu Zhaolian , Rodriguez Judith S. , Ahn Tae-Hyuk , Lin Zhenguo 
Published: January 2019

AbstractThe transcription initiation landscape of eukaryotic genes is complex and highly dynamic. In eukaryotes, genes can generate multiple transcript variants that differ in 5’ boundaries due to usages of alternative transcription start sites (TSSs), and the abundance of transcript isoforms are highly variable. Due to a large number and complexity of the TSSs, it is not feasible to depict details of transcript initiation landscape of all genes using text-format genome annotation files. Therefore, it is necessary to provide data visualization of TSSs to represent quantitative TSS maps and the core promoters. In addition, the selection and activity of TSSs are influenced by various factors, such as transcription factors, chromatin remodeling, and histone modifications. Thus, integration and visualization of functional genomic data related to these features could provide a better understanding of the gene promoter architecture and regulatory mechanism of transcription initiation. Yeast species play important roles for the research and human society, yet no database provides visualization and integration of functional genomic data in yeast. Here, we generated quantitative TSS maps for twelve important yeast species, inferred their core promoters, and built a public database, YeasTSS (www.yeastss.org). YeasTSS was designed as a central portal for visualization and integration of the TSS maps, core promoters and functional genomic data related to transcription initiation in yeast. YeasTSS is expected to benefit the research community and public education for improving genome annotation, studies of promoter structure, regulated control of transcription initiation and inferring gene regulatory network.
The spread of resistance to imidacloprid is restricted by thermotolerance in natural populations ofDrosophila melanogaster
Authors: Fournier-Level Alexandre , Good Robert T , Wilcox Stephen , Rane Rahul V , Schiffer Michelle , Chen Wei , Battlay Paul , Perry Trent , Batterham Philip , Hoffmann Ary A , Robin Charles 
Published: January 2019

AbstractImidacloprid, the world’s most utilised insecticide1, has raised considerable controversy due to its harmful effects on non-pest species2–6and there is increasing evidence showing that insecticides have become the primary selective force in many insect species7–14. The genetic response to insecticides is heterogeneous across population and environment15–17, leading to more complex patterns of genetic variation than previously thought. This motivated the investigation of imidacloprid resistance at different temperatures in natural populations ofDrosophila melanogasteroriginating from four climate extremes replicated across two continents. Population and quantitative genomic analysis, supported by functional tests, demonstrated a polygenic basis to resistance and a major trade-off with thermotolerance. Reduced genetic differentiation at resistance-associated loci indicate enhanced gene flow at these loci. Resistance alleles showed stronger evidence of positive selection in temperate populations compared to tropical populations. Polygenic architecture and ecological factors should be considered when developing sustainable management strategies for both pest and beneficial insects.
The genetic basis of cis-regulatory divergence between the subspecies of cultivated rice (Oryza sativa)
Authors: Campbell Malachy T , Du Qian , Liu Kan , Sharma Sandeep , Zhang Chi , Walia Harkamal 
Published: January 2019

AbstractCultivated rice consists of two subspecies,IndicaandJaponica, that exhibit well-characterized differences at the morphological and genetic levels. However, the differences between these subspecies at the transcriptome level remains largely unexamined. Here, we provide a comprehensive characterization of transcriptome divergence and cis-regulatory variation within rice using transcriptome data from 91 accessions from a rice diversity panel (RDP1). The transcriptomes of the two subspecies of rice are highly divergent. The expression and genetic diversity was significantly lower withinJaponicarelative toIndica, which is consistent with the known population bottleneck duringJaponicadomestication. Moreover, 1,860 and 1,325 genes showed differences in heritability in the broad and narrow sense respectively, between the subspecies, which was driven largely by environmental and genetic effects rather than differences in phenotypic variability. We leveraged high-density genotypic data and transcript levels to identify cis-regulatory variants that may explain the genetic divergence between the subspecies. We identified significantly more eQTL that were specific to theIndicasubspecies compared toJaponica, suggesting that the observed differences in expression and genetic variability also extends to cis-regulatory variation. We next explored the potential causes of this cis-regulatory divergence by assessing local genetic diversity for cis-eQTL. Local genetic diversity around subspecies-specific cis-eQTL was significantly lower than genome-wide averages in subspecies lacking the eQTL, suggesting that selective pressures may have shaped regulatory variation in each subspecies. This study provides the first comprehensive characterization of transcriptional and cis-regulatory variation in cultivated rice, and could be an important resource for future studies.
Annotated bacterial chromosomes from frame-shift-corrected long read metagenomic data
Authors: Arumugam Krithika , Bağci Caner , Bessarab Irina , Beier Sina , Buchfink Benjamin , Gorska Anna , Qiu Guanglei , Huson Daniel H , Williams Rohan BH 
Published: January 2019

AbstractBackgroundShort-read sequencing technologies have long been the work-horse of microbiome analysis. Continuing technological advances are making the application of long-read sequencing to metagenomic samples increasingly feasible.ResultsWe demonstrate that whole bacterial chromosomes can be obtained from a complex community, by application of MinION sequencing to a sample from an EBPR bio-reactor, producing 6Gb of sequence that assembles in to multiple closed bacterial chromosomes. We provide a simple pipeline for processing such data, which includes a new approach to correcting erroneous frame-shifts.ConclusionsAdvances in long read sequencing technology and corresponding algorithms will allow the routine extraction of whole chromosomes from environmental samples, providing a more detailed picture of individual members of a microbiome.
EHD2-mediated restriction of caveolar dynamics regulates cellular lipid uptake
Authors: Matthäus Claudia , Lahmann Ines , Kunz Séverine , Jonas Wenke , Melo Arthur Alves , Lehmann Martin , Larsson Elin , Lundmark Richard , Kern Matthias , Blüher Matthias , Müller Dominik N. , Haucke Volker , Schürmann Annette , Birchmeier Carmen , Daumke Oliver 
Published: January 2019

AbstractEpsl5-homology domain containing protein 2 (EHD2) is a dynamin-related ATPase located at the neck of caveolae, but its physiological function has remained unclear. Here, we found that global genetic ablation of EHD2 in mice led to increased fat accumulation. This organismic phenotype was paralleled at the cellular level by increased lipid uptake via a caveolae-, dynamin- and CD36-dependent pathway, an elevated number of detached caveolae and higher caveolar mobility. Furthermore, EHD2 expression itself was down-regulated in the visceral fat of two obese mouse models and obese patients. Our data suggest that EHD2 controls a cell-autonomous, caveolae-dependent lipid uptake pathway and suggest that low EHD2 expression levels are linked to obesity.
Abl signaling shapes the intrinsic fluctuations of actin to direct growth of a pioneer axon in Drosophila
Authors: Clarke Akanni , McQueen Philip G. , Fang Hsiao Yu , Kannan Ramakrishnan , Wang Victor , McCreedy Evan , Wincovitch Stephen , Giniger Edward 
Published: January 2019

AbstractThe fundamental problem in axon growth and guidance is to understand how cytoplasmic signaling modulates the cytoskeleton to produce directed growth cone motility. We show here that the TSM1 pioneer axon of Drosophila extends by using Abl tyrosine kinase to shape the intrinsic fluctuations of a mass of accumulated actin in the distal axon. The actin mass fluctuates stochastically in length, but with a small, forward bias that drives the axon along its trajectory by promoting emergence of protrusions in leading intervals where actin accumulates, and collapse of protrusions in lagging intervals that actin has vacated. The actin mass is sculpted by Abl signaling, which probabilistically modulates its key parameters - its width and internal disorder - to drive its advance, while maintaining internal coherence. Comparison of TSM1 to other systems suggests that the mechanism we demonstrate here is apt to be common among pioneer axons in many organisms.
The technical support of nanoart: anodization process
Authors: Lv Shaohua , Wang Jian 
Published: January 2019

PurposeThe novel structures and properties of nanostructure and nanomaterials give people perfect artistic expression of feeling and sense, then the nanoart discipline is developed and is closely related on the nanotechniques. The many achieved novel nanostructures with strong anti-corrosion prepared by the anodization have been reviewed. The paper would raise public awareness of nanotechnology, nanomaterial and their impact on our lives.Design/methodology/approachAnodization is a very effective and simple technique to form various nanostructures of metal oxide. It includes hard anodization, mild anodization and pulse anodization. Many measures have been introduced anodization process to improve the quality of formed nanostructure and enhance its properties, such as anti-corrosion.FindingsThe formation mechanism of anodic aluminum oxide (AAO) by using the mild, hard and pulse anodization has been discussed. The pretexture process and many other measures have been taken in mild and hard anodization to improve the regularity of pore array and greatly accelerate the formation rate of AAO. The pulse anodization has been used to prepare the multilayer Y-branched AAO film, which exhibits steady rich and vivid structure colors and gives a very good artistic expression. Furthermore, many other metal oxide nanostructures such as TiO2and CuO have also been fabricated using the anodization techniques.Originality/valueVarious nanostructures of metal oxide prepared by anodization have been reviewed and are itself a perfect artwork in mesoscale. Also, many nanostructures have exhibited steady, rich and vivid structure colors and give people a very good artistic expression.