bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decoding topologically associating domains with ultra-low resolution Hi-C data by graph structural entropy
Authors: Li Angsheng , Yin Xianchen , Xu Bingxiang , Wang Danyang , Han Jimin , Wei Yi , Deng Yun , Xiong Ying , Zhang Zhihua 
Published: August 2018

AbstractSubmegabase-size topologically associating domains (TAD) have been observed in high-throughput chromatin interaction data (Hi-C). However, accurate detection of TADs depends on ultra-deep sequencing and sophisticated normalization procedures. Here we propose a fast and normalization-free method to decode the domains of chromosomes (deDoc) that utilizes structural information theory. By treating Hi-C contact matrix as a representation of a graph, deDoc partitions the graph into segments with minimal structural entropy. We show that structural entropy can also be used to determine the proper bin size of the Hi-C data. By applying deDoc to pooled Hi-C data from 10 single cells, we detect megabase-size TAD-like domains. This result implies that the modular structure of the genome spatial organization may be fundamental to even a small cohort of single cells. Our algorithms may facilitate systematic investigations of chromosomal domains on a larger scale than hitherto have been possible.
Identification of Urine Metabolites as Biomarkers of Early Lyme Disease
Authors: Pegalajar-Jurado Adoracion , Fitzgerald Bryna L. , Islam M. Nurul , Belisle John T. , Wormser Gary P. , Waller Kathlene S. , Ashton Laura V. , Webb Kristofor J. , Delorey Mark J. , Clark Rebecca J. , Molins Claudia R. 
Published: August 2018

AbstractMetabolites detectible in human biofluids are attractive biomarkers for the diagnosis of early Lyme disease (ELD), a vector-borne infectious disease. Urine represents an easily obtained clinical sample that can be applied for diagnostic purposes. However, few studies have explored urine for biomarkers of ELD. In this study, metabolomics approaches were applied to evaluate small molecule metabolites in urine from patients with ELD (n = 14), infectious mononucleosis (n = 14) and healthy controls (n = 14). Metabolic biosignatures for ELD versus healthy controls and ELD versus infectious mononucleosis were generated using untargeted metabolomics. Pathway analyses and metabolite identification revealed the dysregulation of several metabolic processes in ELD as compared to healthy controls or mononucleosis, including metabolism of tryptophan. Linear discriminant analyses demonstrated that individual metabolic biosignatures can correctly discriminate ELD from the other patient groups with accuracies of 71 to 100%. These data provide proof-of-concept for use of urine metabolites as biomarkers for diagnostic classification of ELD.
Long non-coding RNA HOTAIR promotes tumorigenesis and forecasts a poor prognosis in cholangiocarcinoma
Authors: Qin Wei , Kang Pengcheng , Xu Yi , Leng Kaiming , Li Zhenglong , Huang Lining , Gao Jianjun , Cui Yunfu , Zhong Xiangyu 
Published: August 2018

AbstractCholangiocarcinoma (CCA) arising from the neoplastic transformation of cholangiocytes with increasing incidence in the worldwide. Unfortunately, a large amount of CCA patients lost their chance for surgery because it is hard to diagnose in the early stages. Long non-coding RNAs (lncRNAs) is closely associated with development and progression of various malignant tumors. Hox transcript antisense intergenic (HOTAIR), a negative prognostic factor for patients with gastric, liver and pancreatic carcinoma. Its transcription levels and functional roles in CCA is still unknown. Therefore, we aimed to explore the effect of HOTAIR in CCA including cell proliferation, apoptosis, migration, invasion and epithelial-to-mesenchymal transition (EMT). The results showed that HOTAIR was highly expressed both in CCA tissue samples and cell lines compared with corresponding normal bile duct tissues and Human intrahepatic biliary epithelial cells (HIBEC). Its overexpression was closely correlated with Tumor size, TNM stage and postoperative recurrence in CCA patients. Moreover, up-regulation of HOTAIR has correlation with prognosis in CCA patients. Knockdown of HOTAIR by siRNAs significantly decreased the migration and invasion but increased apoptosis of CCA cells in vitro. Overall, our study revealed that HOTAIR may play as a new potential therapeutic target and forecast poor prognosis for this fatal disease.
Exciton physics and device application of two-dimensional transition metal dichalcogenide semiconductors
Authors: Mueller Thomas , Malic Ermin 
Published: August 2018

AbstractTwo-dimensional group-VI transition metal dichalcogenide semiconductors, such as MoS2, WSe2, and others, exhibit strong light-matter coupling and possess direct band gaps in the infrared and visible spectral regimes, making them potentially interesting candidates for various applications in optics and optoelectronics. Here, we review their optical and optoelectronic properties with emphasis on exciton physics and devices. As excitons are tightly bound in these materials and dominate the optical response even at room-temperature, their properties are examined in depth in the first part of this article. We discuss the remarkably versatile excitonic landscape, including bright, dark, localized and interlayer excitons. In the second part, we provide an overview on the progress in optoelectronic device applications, such as electrically driven light emitters, photovoltaic solar cells, photodetectors, and opto-valleytronic devices, again bearing in mind the prominent role of excitonic effects. We conclude with a brief discussion on challenges that remain to be addressed to exploit the full potential of transition metal dichalcogenide semiconductors in possible exciton-based applications.
Metamaterial‐based circularly polarised antenna employing ENG‐TL with enhanced bandwidth for WLAN applications
Authors: Ameen M. , Chaudhary R.K. 
Published: August 2018

This work explains the design and development of a low profile and compact single probe‐fed metamaterial (MTM)‐based circularly polarised (CP) antenna using the modified rectangular patch with two pairs of spiral strips and vias for 5.2/5.8 GHz WLAN applications. The intended CP antenna mainly consists of two pairs of radiators and each radiator is realised by using epsilon negative (ENG) transmission line (TL) to generate zeroth‐order resonance. CP characteristics are achieved by placing two radiators for x‐polarised wave are orthogonally aligned to the other two radiators for y‐polarised wave. The antenna radiating element offers a compact size of 0.24λ0 × 0.22λ0 with a low profile of 0.04λ0 at 5.5 GHz. To confirm the characteristics of the intended MTM CP antenna design, the designed antenna is fabricated and measured. Measurement results show that the antenna obtains −10 dB impedance bandwidth of 610 MHz (10.86%) which is 2.3 times larger than the standard microstrip patch antenna and axial ratio bandwidth of 140 MHz (2.54%) is obtained.
Timing of Tracheostomy in Intensive Care Unit Patients
Authors: Khammas Ammar , Dawood Mohammed 
Published: August 2018

Introduction The ideal timing of tracheostomy in intensive care units (ICUs) for critically ill patients undergoing prolonged mechanical ventilation (MV) is still a controversial issue.
Objectives To determine the proper timing of tracheostomy and its impact on various clinical outcomes of adult patients in ICUs undergoing prolonged MV.
Methods The present study consisted of a sample of 67 ICU adult patients who were submitted to open surgical tracheostomy and divided into two groups: 30 patients in the early tracheostomy (ET) group (within 1–10 days post intubation), and 37 patients in the late tracheostomy (LT) group (within 11–21 days post intubation). The correlation between the timing of tracheostomy of each group and various associated ICU clinical parameters were analyzed.
Results The sample consisted of 61.19% male and 38.81% female patients, with a mean age of 47.263 ± 7.581 years. The mean MV duration in days was 7.91 ± 4.937 standard deviation (SD) in the ET group, and 15.32 ± 7.472 SD in the LT group (p = 0.001), with a mean sedation time of 6.13 ± 4.647 SD in the ET group, and of 11.98 ± 6.596 SD in the LT group (p = 0.001). The duration of the weaning process duration had a mean of 2.75 ± 2.586 SD days in the ET group, and of 5.39 ± 5.817 SD days in the LT group (p = 0.025), with a weaning failure rate of 28.57% in the ET group and 71.42% in the LT group (p = 0.01). The Mean ICU stay was 26.18 ± 4.732 SD in the ET group, and 11.98 ± 6.596 SD in the LT group (p = 0.879), and the incidence of ventilator-associated pneumonia (VAP) of 23.33% in the ET group and of 27.02% in the LT group (p = 0.15).
Conclusion Early tracheostomy had a notable benefit in shortening the duration of the MV, lessening the sedation time and minimizing the risks of weaning failure, but it had no significant impact on both the overall duration of ICU stay and VAP incidence.
An Unusual Case of Noncatamenial Recurrent Pneumothorax
Authors: Kirschbaum Andreas , Greulich Timm , Mirow Nikolas , Bartsch Detlef 
Published: August 2018

AbstractIn a 28-year-old female, seven recurrent pneumothoraces occurred during a period of 2 years despite multiple thoracic interventions, all on the left thoracic side. Despite profound differential diagnostic analysis, the underlying cause remains unclear. An accumulation of conditions in this patient affecting only the left half of the body is remarkable: sinistral glaucoma as an infant, a sinistral pigmentation disorder, and a sinistral Bochdalek hernia.
Surgical Treatment of Cardiac Metastases: Analysis of a 13-Year Single-Center Experience
Authors: Mkalaluh Sabreen , Szczechowicz Marcin , Torabi Saeed , Sabashnikov Anton , Mashhour Ahmed , Karck Matthias , Weymann Alexander 
Published: August 2018

Background Cardiac metastases are more common than primary malignant tumors of the heart and are usually treated surgically as a palliative approach. In this study, we reviewed our experience with the surgical treatment of patients with cardiac metastases of various types of malignant tumors.
Methods Between 2003 and 2016, 10 patients underwent surgery for cardiac metastases at our institution.
Results The mean age was 53.5 ± 19 years. Female patients made up 60% (n = 6) of the collective. The cohort included cardiac metastases of diverse origins (peripheral sarcomas, melanoma, rectal carcinoma, and hepatocellular carcinoma). The left side of the heart was more frequently affected (n = 7). In only six patients, the primary malignancy was known at the time of cardiac surgery. The interval between the first diagnosis of the primary tumor and cardiac metastases ranged from simultaneous diagnosis to up to 19 years. At the time of the diagnosis of the cardiac metastases, seven patients already had multiple metastases: all seven patients had pulmonary metastases, and three of them additionally had hepatic, cerebral, or osseous metastases. Only four patients were symptomatic (atrial fibrillation, pericardial effusion, tachycardia with chest pain, dyspnea). There was no in-hospital death. The postoperative course was uneventful overall. The one- and two-year survival rates were similar, that is, 76%. The median follow-up time was 5.4 years.
Conclusions Surgical intervention for treating cardiac metastases is associated with uneventful clinical outcome and acceptable survival in this critically ill population. Control of the primary malignancy, and maybe other metastases, determines the survival.
Elucidation of near-resonance vibronic coherence lifetimes by nonadiabatic electronic-vibrational state character mixing
Authors: Yeh Shu-Hao , Hoehn Ross D. , Allodi Marco A. , Engel Gregory S. , Kais Sabre 
Published: August 2018

Significance
Excitation energy transfer (EET) remains one of the most highly discussed nonequilibrium transport phenomena in the fields of biophysics and physical chemistry because of the possible role of long-lived quantum coherences in enhancing transport efficiency. These coherences were first observed using 2D electronic spectroscopy, and their origin remains elusive. By modeling a vibronically coupled dimer with explicitly introduced dephasing mechanisms—such as electronic energy fluctuation and vibrational relaxation—we demonstrate that the coherence lifetime is highly correlated with the degree of electronic-vibrational mixing, implying that near the exciton-vibrational resonance, the vibronic system has an optimal balance between coherence lifetime and oscillator strength. The degree of vibronic coupling may thus be an optimizable parameter to enhance energy transfer.
Market Concentration, Market Shares, and Retail Food Prices: Evidence from the U.S. Women, Infants, and Children Program
Authors: Ma Meilin , Saitone Tina L. , Volpe Richard J. , Sexton Richard J. , Saksena Michelle 
Published: August 2018

AbstractWe explore pricing in local food‐retailing markets where supermarkets operate versus those occupied solely by smaller food retailers. Using data from the Women, Infants, and Children program in the Greater Los Angeles area, we show that supermarkets do not raise prices in local markets or as a function of market concentration or firm market shares. Smaller food retailers charge substantially higher prices on average than supermarkets. Their prices increase with market concentration and shares of sales, especially when small retailers face no direct competition from supermarkets. Given the dominance of small retailers in some low‐income areas, our findings have important implications regarding local market power, food costs, and supermarket entry.
The Effect of California’s Paid Family Leave Program on Employment Among Middle-Aged Female Caregivers
Authors: Kang Ji Young , Park Sojung , Kim BoRin , Kwon Eunsun , Cho Joonyoung 
Published: August 2018

Abstract

Background and Objectives
This study examined the effect of a Paid Family Leave program in California (CA-PFL) on employment among middle-aged female caregivers. We also examined differences in the relationship between the availability of paid family leave (PFL) and employment in socioeconomic subgroups of midlife women.

Research Design and Methods
Data came from multiple years (2000‒2014) of the Current Population Survey (CPS) (N = 68,773 individuals). Applying a Difference in Differences (DiD) approach to removing potential selection biases related to program participation, we used a logistic regression to estimate the effects of PFL.

Results
There was a significant increase in the likelihood of working based on CA-PFL. This positive effect, however, was found only among the early middle-aged, the near-poor, and those had the highest level of education.

Discussion and Implications
Among the late middle-aged, caregiving burden may not affect decisions on whether to exit the labor market, and PFL may not significantly mitigate the well-known negative effects of intense and multiple caregiving roles (parents, spouse, and/or children with disabilities). Future studies should examine PFL effects and their correlates such as age-cohorts, caregiving intensity, and retirement patterns. The unexpected null findings of CA-PFL’s effect on employment outcomes for the poor and those with low education levels suggests these vulnerable groups might not be able to fully benefit from the originally intended goal of the policy, instead being left more vulnerable compared to the near poor. Such a possibility increases the importance of focused research and policymaking attention for this group.
Comparisons of echo-integration performance from two multiplexed echosounders
Authors: Macaulay Gavin J , Scoulding Ben , Ona Egil , Fässler Sascha M M 
Published: August 2018

Abstract
A time-series of acoustically derived aquatic biomass estimates relies on the acoustic equipment maintaining the same performance throughout the time-series. This is normally achieved through a regular calibration process. When the acoustic equipment changes it is necessary to verify that the new equipment produces a similar result to the old equipment, otherwise an unknown bias can be introduced into the time-series. The commonly used Simrad EK60 echosounder has been superseded by the Simrad EK80 echosounder and the performance of these two scientific echosounder systems was compared using interleaved pinging through the same transducer. This was repeated for multiple transducer frequencies (18, 38, 70, 120, and 200 kHz) and from two vessels (Norway’s G.O. Sars in the North Sea and The Netherlands’ Tridens in the Northeast Atlantic Ocean). The broadband facility of the EK80 was not used. Regressions of the grid-integrated backscatter from the two systems were highly linear. The difference in area backscattering coefficients in typical survey conditions was less than 0.6 dB (12%) at the main survey frequency of 38 kHz. In most conventional fish acoustic surveys, the observed differences are less than other sources of survey bias and uncertainty.
Biomedical informatics meets data science: current state and future directions for interaction
Authors: Payne Philip R O , Bernstam Elmer V , Starren Justin B 
Published: August 2018

Abstract
There are an ever-increasing number of reports and commentaries that describe the challenges and opportunities associated with the use of big data and data science (DS) in the context of biomedical education, research, and practice. These publications argue that there are substantial benefits resulting from the use of data-centric approaches to solve complex biomedical problems, including an acceleration in the rate of scientific discovery, improved clinical decision making, and the ability to promote healthy behaviors at a population level. In addition, there is an aligned and emerging body of literature that describes the ethical, legal, and social issues that must be addressed to responsibly use big data in such contexts. At the same time, there has been growing recognition that the challenges and opportunities being attributed to the expansion in DS often parallel those experienced by the biomedical informatics community. Indeed, many informaticians would consider some of these issues relevant to the core theories and methods incumbent to the field of biomedical informatics science and practice. In response to this topic area, during the 2016 American College of Medical Informatics Winter Symposium, a series of presentations and focus group discussions intended to define the current state and identify future directions for interaction and collaboration between people who identify themselves as working on big data, DS, and biomedical informatics were conducted. We provide a perspective concerning these discussions and the outcomes of that meeting, and also present a set of recommendations that we have generated in response to a thematic analysis of those same outcomes. Ultimately, this report is intended to: (1) summarize the key issues currently being discussed by the biomedical informatics community as it seeks to better understand how to constructively interact with the emerging biomedical big data and DS fields; and (2) propose a framework and agenda that can serve to advance this type of constructive interaction, with mutual benefit accruing to both fields.
Clinical Impact of Tumor Mutational Burden in Neuroblastoma
Authors: Hwang William L , Wolfson Rachel L , Niemierko Andrzej , Marcus Karen J , DuBois Steven G , Haas-Kogan Daphne 
Published: August 2018

Abstract

Background
Neuroblastoma is the most common pediatric extracranial solid tumor. Within conventional risk groups, there is considerable heterogeneity in outcomes, indicating the need for improved risk stratification.

Methods
In this study we analyzed the somatic mutational burden of 515 primary, untreated neuroblastoma tumors from three independent cohorts. Mutations in coding regions were determined by whole-exome/genome sequencing of tumor samples compared to matched blood leukocytes. Survival data for 459 patients were available for analysis of 5-year overall survival using the Kaplan–Meier method and log-rank test. All statistical tests were two-sided.

Results
Despite a low overall somatic mutational burden (mean = 3, range = 0–56), 107 patients were considered to have high mutational burden (>3 mutations). Unfavorable histology and age 18 months and older were associated with high mutational burden. Patients with high mutational burden had inferior 5-year overall survival (29.0%, 95% confidence interval [CI] = 17.2 to 41.8%) vs those with three or fewer somatic mutations (76.2%, 95% CI = 71.5 to 80.3%) (log-rank P < .001) and this association persisted when limiting the analysis to genes included on a 447-gene panel commonly used in clinical practice. On multivariable analysis, mutational burden remained prognostic independent of age, stage, histology and MYCN status.

Conclusions
This study demonstrates that mutational burden of primary neuroblastoma may be useful in combination with conventional risk factors to optimize risk stratification and guide treatment decisions, pending prospective validation.
ALMA imaging of the nascent planetary nebula IRAS 15103–5754
Authors: Gómez José F , Niccolini Gilles , Suárez Olga , Miranda Luis F , Rizzo J Ricardo , Uscanga Lucero , Green James A , de Gregorio-Monsalvo Itziar 
Published: August 2018

ABSTRACT
We present continuum and molecular-line (CO, C18O, HCO+) observations carried out with the Atacama Large Millimeter/submillimeter Array toward the ‘water fountain’ star IRAS 15103–5754, an object that could be the youngest planetary nebula (PN) known. We detect two continuum sources, separated by 0.39 ± 0.03 arcsec. The emission from the brighter source seems to arise mainly from ionized gas, thus confirming the PN nature of the object. The molecular-line emission is dominated by a circumstellar torus with a diameter of ≃0.6 arcsec (2000 au) and expanding at ≃23 km s−1. We see at least two gas outflows. The highest-velocity outflow (deprojected velocities up to 250 km s−1), traced by the CO lines, shows a biconical morphology, whose axis is misaligned ≃14° with respect to the symmetry axis of the torus, and with a different central velocity (by ≃8 km s−1). An additional high-density outflow (traced by HCO+) is oriented nearly perpendicular to the torus. We speculate that IRAS 15103–5754 was a triple stellar system that went through a common envelope phase, and one of the components was ejected in this process. A subsequent low-collimation wind from the remaining binary stripped out gas from the torus, creating the conical outflow. The high velocity of the outflow suggests that the momentum transfer from the wind is extremely efficient, or that we are witnessing a very energetic mass-loss event.
Prince Paul’s Psychoanalysis: What Is It?
Authors: Fleshner Nathan 
Published: August 2018

Abstract
This chapter provides an analysis of Prince Paul’s album Psychoanalysis: What Is It? in the context of Sigmund Freud’s psychoanalytic process and focuses on three key tenets of that process—free association, transference, and drives. It explores not only a satirical therapeutic process in Paul’s album but also a commentary on and critique of the psychoanalytic process itself—a judgment on the effectiveness of a therapeutic treatment, particularly in regard to race. It frames Psychoanalysis within the context of several of Paul’s subsequent albums and the work of other hip hop artists. In doing so, it builds on previous categorizations of rap topics and style and proposes a new genre, therapy rap.