bluuebunny/crossref_metadata_2025_split huggingface dataset:
TADKB: Family classification and a knowledge base of topologically associating domains
Authors: Liu Tong , Porter Jacob , Zhao Chenguang , Zhu Hao , Wang Nan , Sun Zheng , Mo Yin-Yuan , Wang Zheng 
Published: March 2019

Abstract
Background
Topologically associating domains (TADs) are considered the structural and functional units of the genome. However, there is a lack of an integrated resource for TADs in the literature where researchers can obtain family classifications and detailed information about TADs.

Results
We built an online knowledge base TADKB integrating knowledge for TADs in eleven cell types of human and mouse. For each TAD, TADKB provides the predicted three-dimensional (3D) structures of chromosomes and TADs, and detailed annotations about the protein-coding genes and long non-coding RNAs (lncRNAs) existent in each TAD. Besides the 3D chromosomal structures inferred by population Hi-C, the single-cell haplotype-resolved chromosomal 3D structures of 17 GM12878 cells are also integrated in TADKB. A user can submit query gene/lncRNA ID/sequence to search for the TAD(s) that contain(s) the query gene or lncRNA. We also classified TADs into families. To achieve that, we used the TM-scores between reconstructed 3D structures of TADs as structural similarities and the Pearson’s correlation coefficients between the fold enrichment of chromatin states as functional similarities. All of the TADs in one cell type were clustered based on structural and functional similarities respectively using the spectral clustering algorithm with various predefined numbers of clusters. We have compared the overlapping TADs from structural and functional clusters and found that most of the TADs in the functional clusters with depleted chromatin states are clustered into one or two structural clusters. This novel finding indicates a connection between the 3D structures of TADs and their DNA functions in terms of chromatin states.

Conclusion
TADKB is available at http://dna.cs.miami.edu/TADKB/.
Transcriptome profiling analysis reveals that CXCL2 is involved in anlotinib resistance in human lung cancer cells
Authors: Lu Jun , Xu Wei , Qian Jie , Wang Shuyuan , Zhang Bo , Zhang Lele , Qiao Rong , Hu Minjuan , Zhao Yiming , Zhao Xiaodong , Han Baohui 
Published: March 2019

Abstract
Background
Anlotinib has been demonstrated its anti-tumor efficacy on non-small cell lung cancer (NSCLC) in clinical trials at 3rd line. However, anlotinib resistance occurs during its administration, and the underlying mechanism is still unclear.

Methods
Anlotinib resistant lung cancer cell line NCI-H1975 was established in vitro. Toxicologic effects undergoing anlotinib stress were observed upon NCI-H1975 cells and anlotinib resistant NCI-H1975 cells, respectively. Transcriptome profiling was performed to screen anlotinib resistance-associated genes between NCI-H1975 cells and anlotinib resistant NCI-H1975 cells. Functional assays were performed to examine the correlations between CXCL2 gene expression and anlotinib resistance.

Results
We found anlotinib inhibits cell proliferation and cell viability in NCI-1975 cells, whereas it attenuates these activities in anlotinib resistant NCI-H1975 cells. Transcriptome profiling analysis identified 769 anlotinib-responsive genes enriched in the biological processes of microtubule-based process, cytoskeleton organization, and wound healing. Furthermore, we found 127 genes are associated with anlotinib resistance. In particular, we demonstrated that CXCL2 contributes to anlotinib resistance in NCI-H1975 cells.

Conclusions
This study suggested that CXCL2 is involved in anlotinib resistance in NCI-H1975 cells and provided an insight for understanding the resistant mechanism of anlotinib.
Aluminium and fluoride in drinking water in relation to later dementia risk
Authors: Russ Tom C. , Killin Lewis O. J. , Hannah Jean , Batty G. David , Deary Ian J. , Starr John M. 
Published: March 2019

BackgroundEnvironmental risk factors for dementia are poorly understood. Aluminium and fluorine in drinking water have been linked with dementia but uncertainties remain about this relationship.AimsIn the largest longitudinal study in this context, we set out to explore the individual effect of aluminium and fluoride in drinking water on dementia risk and, as fluorine can increase absorption of aluminium, we also examine any synergistic influence on dementia.MethodWe used Cox models to investigate the association between mean aluminium and fluoride levels in drinking water at their residential location (collected 2005–2012 by the Drinking Water Quality Regulator for Scotland) with dementia in members of the Scottish Mental Survey 1932 cohort who were alive in 2005.ResultsA total of 1972 out of 6990 individuals developed dementia by the linkage date in 2012. Dementia risk was raised with increasing mean aluminium levels in women (hazard ratio per s.d. increase 1.09, 95% CI 1.03–1.15,P< 0.001) and men (1.12, 95% CI 1.03–1.21,P= 0.004). A dose-response pattern of association was observed between mean fluoride levels and dementia in women (1.34, 95% CI 1.28–1.41,P< 0.001) and men (1.30, 95% CI 1.22–1.39,P< 0.001), with dementia risk more than doubled in the highest quartile compared with the lowest. There was no statistical interaction between aluminium and fluoride levels in relation with dementia.ConclusionsHigher levels of aluminium and fluoride were related to dementia risk in a population of men and women who consumed relatively low drinking-water levels of both.
Identifying Women at High Risk for Breast Cancer Using Data From the Electronic Health Record Compared With Self-Report
Authors: Jiang Xinyi , McGuinness Julia E. , Sin Margaret , Silverman Thomas , Kukafka Rita , Crew Katherine D. 
Published: March 2019

PURPOSE A barrier to chemoprevention uptake among high-risk women is the lack of routine breast cancer risk assessment in the primary care setting. We calculated breast cancer risk using the Breast Cancer Surveillance Consortium (BCSC) model, accounting for age, race/ethnicity, first-degree family history of breast cancer, benign breast disease, and mammographic density, using data collected from the electronic health records (EHRs) and self-reports. PATIENTS AND METHODS Among women undergoing screening mammography, we enrolled those age 35 to 74 years without a prior history of breast cancer. Data on demographics, first-degree family history, breast radiology, and pathology reports were extracted from the EHR. We assessed agreement between the EHR and self-report on information about breast cancer risk. RESULTS Among 9,514 women with known race/ethnicity, 1,443 women (15.2%) met high-risk criteria based upon a 5-year invasive breast cancer risk of 1.67% or greater according to the BCSC model. Among 1,495 women with both self-report and EHR data, more women with a first-degree family history of breast cancer (14.6% v 4.4%) and previous breast biopsies (21.3% v 11.3%) were identified by self-report versus EHR, respectively. However, more women with atypia and lobular carcinoma in situ were identified from the EHR. There was moderate agreement in identification of high-risk women between EHR and self-report data (κ, 0.48; 95% CI, 0.42-0.54). CONCLUSION By using EHR data, we determined that 15% of women undergoing screening mammography had a high risk for breast cancer according to the BCSC model. There was moderate agreement between information on breast cancer risk derived from the EHR and self-report. Examining EHR data may serve as an initial screen for identifying women eligible for breast cancer chemoprevention.
Orthogonal Comparison of Four Plasma NGS Tests With Tumor Suggests Technical Factors are a Major Source of Assay Discordance
Authors: Stetson Daniel , Ahmed Ambar , Xu Xing , Nuttall Barrett R.B. , Lubinski Tristan J. , Johnson Justin H. , Barrett J. Carl , Dougherty Brian A. 
Published: March 2019

PURPOSE Discordance between plasma and tumor variant calling has been attributed primarily to tumor heterogeneity, whereas technical variables remain largely unexplored. MATERIALS AND METHODS To measure these variables, we tested four next-generation sequencing (NGS) gene panel assays for mutations in circulating tumor DNA (ctDNA) using replicate sets of 24 plasma samples and compared the results with matched tumor-normal tissue pairs. RESULTS Our orthogonal approach identified false-negative (FN) and false-positive (FP) variants with high confidence and revealed substantial variability among the ctDNA assays, with a range of sensitivity (38% to 89%) and positive predictive value (36% to 80%). Most discordance in our cross-vendor study was observed below 1% variant allele frequency. FP variants displayed mutational biases and tended to be novel variants not found in somatic databases. Of the 56 unique variants called by all four ctDNA assays, 41 (68%) resulted from technical discordance. CONCLUSION These findings suggest that most NGS assay discordance is a result of technical variations and, to a lesser extent, biologic factors such as clonal hematopoiesis of indeterminate potential and tumor heterogeneity.
Defining developmental diversification of diencephalon neurons through single cell gene expression profiling
Authors: Guo Qiuxia , Li James Y. H. 
Published: March 2019

ABSTRACT
The embryonic diencephalon forms integration centers and relay stations in the forebrain. Anecdotal expression studies suggest that the diencephalon contains multiple developmental compartments and subdivisions. Here, we utilized single cell RNA sequencing to profile transcriptomes of dissociated cells from the diencephalon of E12.5 mouse embryos. We identified the divergence of different progenitors, intermediate progenitors, and emerging neurons. By mapping the identified cell groups to their spatial origins, we characterized the molecular features of cell types and cell states arising from various diencephalic domains. Furthermore, we reconstructed the developmental trajectory of distinct cell lineages, and thereby identified the genetic cascades and gene regulatory networks underlying the progression of the cell cycle, neurogenesis and cellular diversification. The analysis provides new insights into the molecular mechanisms underlying the amplification of intermediate progenitor cells in the thalamus. The single cell-resolved trajectories not only confirm a close relationship between the rostral thalamus and prethalamus, but also uncover an unexpected close relationship between the caudal thalamus, epithalamus and rostral pretectum. Our data provide a useful resource for systematic studies of cell heterogeneity and differentiation kinetics within the diencephalon.
On-Demand Digital Economy: Can Experience Ensure Work and Income Security for Microtask Workers?
Authors: Rani Uma , Furrer Marianne 
Published: March 2019

Abstract
Digital labour platforms have been increasingly gaining popularity over the past decade. In particular, there has been much debate about workers’ motivations and working conditions on microtask platforms. There exists little evidence on whether dependence on digital microtask platforms provides workers with work and income security in the long term and whether it provides opportunities for skill development. This paper explores the extent to which the seemingly flexible platform work ensures work and income security and provides opportunities for skill development for workers with different levels of experience, based on novel survey data collected on five globally operating microtask platforms and in-depth interviews with workers. The findings show that despite high financial dependence on this work, returns to experience on the platform are meagre in terms of earnings, and highly experienced workers face the same risks as new entrants with regard to discrimination, high work intensity, lack of autonomy and control over work, and social protection. There is also a skills gap between the nature of tasks available on these microtask platforms and the workers’ education levels. Finally, experience does not ensure that workers have the opportunities to undertake complex and challenging tasks, and the possibilities to develop their skills and improve career prospects are limited.
A need-adapted transition program after pediatric kidney transplantation
Authors: Rieger Susanne , Bethe Dirk , Bagorda Angela , Treiber Dorothea , Beimler Jörg , Sommerer Claudia , Höcker Britta , Fichtner Alexander , Vinke Tobias , Zeier Martin , Hoffmann Georg Friedrich , Tönshoff Burkhard 
Published: March 2019

AbstractA successful transition of renal transplant recipients from pediatric to adult care requires a structured, need-adapted and multidisciplinary approach to preserve renal graft function during this critical period of life. In this article we present our clinical protocol for transition from pediatric to adult care, which we developed on the basis of the International Society of Nephrology (ISN)/International Pediatric Nephrology Association (IPNA) consensus guidelines influenced by our own experience. This transition program was established in our center in July 2017. The entire transition process is structured and accompanied by a transition key worker (social worker). From 12 years of age we train pediatric renal transplant recipients in medical knowledge, self-management skills and networking with self-help groups. The training is adapted to the individual patient‘s intellectual ability, lasts about 10 years and takes place with increasing intensity. Repeatedly we perform standardized informational interviews and check patient’s knowledge of transplant-related topics. Psychosocial and educational issues are evaluated concomitantly. The actual transfer takes place in a pediatric-adult-transition clinic. Relevant medical and psychosocial aspects are discussed and the future treatment regimen is established. The date of transfer is adapted to the individual patient’s need; it varies between 18 and 24 years of age. In periods of increased risk for non-adherence the transfer is postponed to intensify the efforts for training and assistance. After transfer a standardized evaluation of each individual patient takes place focusing on medical and psychosocial issues and on satisfaction with the transition process. Collection of these data is still in progress and will be analyzed systematically at a later stage in order to evaluate the impact of this new transition program on the stability of transplant function. That analysis might serve as a basis for negotiations about refunding with health insurance companies.
Time-dependent attractor of wave equations with nonlinear damping and linear memory
Authors: Ma Qiaozhen , Wang Jing , Liu Tingting 
Published: March 2019

Abstract
In this article, we consider the long-time behavior of solutions for the wave equation with nonlinear damping and linear memory. Within the theory of process on time-dependent spaces, we verify the process is asymptotically compact by using the contractive functions method, and then obtain the existence of the time-dependent attractor in

$\begin{array}{}
H^{1}_0({\it\Omega})\times L^{2}({\it\Omega})\times L^{2}_{\mu}(\mathbb{R}^{+};H^{1}_0({\it\Omega}))
\end{array}$.
Effect of Foliar Application of Boron with Calcium and Potassium on Quality and Yield of Mango cv. Summer Bahisht (SB) Chaunsa
Authors: Bibi Fatma , Ahmad Iftikhar , Bakhsh Allah , Kiran Sidra , Danish Subhan , Ullah Hameed , Rehman Asif-ur 
Published: March 2019

AbstractPoor uptake of nutrients not only deteriorates the quality but also the yield of horticultural crops. Among various macro and micronutrients, the role of K, Ca and B is very important. Therefore, balanced application and uptake of K and Ca and B can improve the quality and yield of mango trees. So, a field study was conducted with the hypothesis that combined application of K and Ca along with B would be effective to improve yield and quality of Mango cv. Summer Bahisht (SB) Chaunsa. There were two sources of Ca(CaCl2 and Ca(NO3)2) and three sources of K(KNO3, K2SO4 and K-Citrate) combined with boric acid (BA). All Ca and K sources were applied at the rate of 1% while BA was applied at 0.2%. As compared to control, a significant improvement in fruit set panicle-1 (35.7% and 50.0%), fruit retention (125% and 40%), shelf life (73.3% and 36.6%), total soluble solids (35.1% and 40.6%) and fruit yield (52.5% and 49.2%) in 2016 and 2017 respectively, confirmed the effectiveness of KNO3 (1.0%) + BA (0.2%). Between CaCl2 and Ca(NO3)2, application of Ca (NO3)2 was found more efficacious regarding improvement of quality and yield of SB Chaunsa. It is concluded that to improve the quality and yield of Mango cv. SB Chaunsa, KNO3 (1.0%) + BA (0.2%) is the best nutrients combination, and Ca(NO3)2 is a better option as compared to CaCl2.
Interactive robots with model-based ‘autism-like’ behaviors
Authors: Baraka Kim , Melo Francisco S. , Veloso Manuela 
Published: March 2019

Abstract
Due to their predictability, controllability, and simple social abilities, robots are starting to be used in diverse ways to assist individuals with Autism Spectrum Disorder (ASD). In this work, we investigate an alternative and novel research direction for using robots in relation to ASD, through programming a humanoid robot to exhibit behaviors similar to those observed in children with ASD. We designed 16 ‘autism-like’ behaviors of different severities on a NAO robot, based on ADOS-2, the gold standard for ASD diagnosis. Our behaviors span four dimensions, verbal and non-verbal, and correspond to a spectrum of typical ASD responses to 3 different stimulus families inspired by standard diagnostic tasks. We integrated these behaviors in an autonomous agent running on the robot, with which humans can continuously interact through predefined stimuli. Through user-controllable features, we allow for 256 unique customizations of the robot’s behavioral profile.We evaluated the validity of our interactive robot both in video-based and ‘in situ’ studies with 3 therapists. We also present subjective evaluations on the potential benefits of such robots to complement existing therapist training, as well as to enable novel tasks for ASD therapy.
Evaluation und Justierung eines neuartigen, hochfrequent fokusabstandsmodulierten, fasergekoppelten, konfokalen Punktsensors für axial geregelte Oberflächenmessungen mit einem Nanokoordinatenmessgerät
Authors: Gröschl Andreas Christian , Schaude Janik , Hausotte Tino 
Published: March 2019

Zusammenfassung
In diesem Artikel wird ein neues Messverfahren zur Oberflächenmessung bei gleichzeitiger axialer Regelung des Arbeitsabstandes eines hochfrequent fokusabstandsmodulierten, fasergekoppelten, konfokalen Punktsensors in einem Nanokoordinatenmessgerät (NMM-1) [T. Hausotte, B. Percle, and G. Jäger. Meas. Sci. Technol., 2009] vorgestellt. Während bei diesem Verfahren alle bekannten Vorteile der Konfokaltechnik beibehalten werden, stellt die innovative Kombination einer fasergekoppelten Beleuchtung und Detektion mit einer akustisch getriebenen, modulierbaren Flüssigkeitsgradientenlinse (engl. tuneable, acoustically driven gradient-index fluid lens, Abk. TAG-Linse) [Tag Optics Inc. Datasheet, 2013] zur hochfrequenten Abstandmodulation des Fokus zusammen mit einer neuartigen Signalverarbeitung auf Basis einer Lock-in-Verstärkung eine wesentliche Verbesserung dar. Durch die Anordnung und Auswertung ergibt sich im Gegensatz zu konventionellen konfokalen Punktsensoren eine nahezu lineare Kennlinie, wobei die Richtung der Abweichung der Messobjektoberfläche relativ zur Fokusebene des Objektivs eindeutig bestimmt werden kann. Es wird insbesondere die Verwendung des Sensors sowie die Nutzung der resultierenden Kennlinie zur Regelung der Oberflächenposition in einem Nanokoordinatenmessgerät gezeigt. Im Gegensatz zum Verfahren konventioneller Konfokalsensoren, bei der lateral flächenhafte Abtastungen auf vielen diskreten axialen Höhen durchgeführt werden, um daraus für jeden lateralen Messpunkt durch eine Maximalwertsuche einen Höhenwert zu ermitteln, kann durch die gezeigte Nachregelung eine Oberflächenerfassung durch eine einzige laterale Abstastung erfolgen. Die sich daraus ergebende immense Zeitersparnis führt zusätzlich zu Messungen mit geringeren thermischen Driften und geringeren Messabweichungen.
Oas1b-dependent Immune Transcriptional Profiles of West Nile Virus Infection in the Collaborative Cross
Authors: Green Richard , Wilkins Courtney , Thomas Sunil , Sekine Aimee , Hendrick Duncan M , Voss Kathleen , Ireton Renee C , Mooney Michael , Go Jennifer T , Choonoo Gabrielle , Jeng Sophia , de Villena Fernando Pardo-Manuel , Ferris Martin T , McWeeney Shannon , Gale Michael 
Published: March 2019

Abstract
The oligoadenylate-synthetase (Oas) gene locus provides innate immune resistance to virus infection. In mouse models, variation in the Oas1b gene influences host susceptibility to flavivirus infection. However, the impact of Oas variation on overall innate immune programming and global gene expression among tissues and in different genetic backgrounds has not been defined. We examined how Oas1b acts in spleen and brain tissue to limit West Nile virus (WNV) susceptibility and disease across a range of genetic backgrounds. The laboratory founder strains of the mouse Collaborative Cross (CC) (A/J, C57BL/6J, 129S1/SvImJ, NOD/ShiLtJ, and NZO/HlLtJ) all encode a truncated, defective Oas1b, whereas the three wild-derived inbred founder strains (CAST/EiJ, PWK/PhJ, and WSB/EiJ) encode a full-length OAS1B protein. We assessed disease profiles and transcriptional signatures of F1 hybrids derived from these founder strains. F1 hybrids included wild-type Oas1b (F/F), homozygous null Oas1b (N/N), and heterozygous offspring of both parental combinations (F/N and N/F). These mice were challenged with WNV, and brain and spleen samples were harvested for global gene expression analysis. We found that the Oas1b haplotype played a role in WNV susceptibility and disease metrics, but the presence of a functional Oas1b allele in heterozygous offspring did not absolutely predict protection against disease. Our results indicate that Oas1b status as wild-type or truncated, and overall Oas1b gene dosage, link with novel innate immune gene signatures that impact specific biological pathways for the control of flavivirus infection and immunity through both Oas1b-dependent and independent processes.
Opinions on the Impacts of the TEOG System from Teachers Whose Courses are not Included in the TEOG Exam
Authors: ULUTAŞ Seher , ÇIKRIKÇI Nükhet 
Published: March 2019

The object of this study is to determine of teachers’ opinions on the impacts of exam for the Transition from Basic Education to Secondary Education TEOG system on their teaching activities in visual arts, technology and design, music and physical education courses that are not covered by the TEOG exam. This research was conducted as a survey study and the study group was determined by the purpose of sampling strategy, data analysis plan and easy accessibility approach. This research was carried out with 35 teachers who teach visual arts, physical education, technology and design, and music courses in public schools in Ankara. Teachers’ opinions were obtained with a form containing five open-ended questions and demographic and occupational characteristics of the teachers. A descriptive analysis approach was applied to the written opinions of the teachers. As a result of this research according to the opinions of teachers; visual arts, technology and design, music and physical education courses which are not included by the TEOG exams were considered to be insignificant by students, school administrators and parents. In addition, teachers stated that the TEOG system affected their teaching and evaluation activities negatively in the classroom, and the teachers were unable to evaluate their students objectively due to the TEOG system, and students, administrators and parents expected or demanded the teacher to give higher grades. Because of these situations, the relations between the teachers, students, school administrators and parents were affected negatively.