Miracle-dz/UniFAR-FTUs huggingface dataset:
Signatures of Planets in Spatially Unresolved Debris Disks

Main-sequence stars are commonly surrounded by debris disks, composed of cold dust continuously replenished by a reservoir of undetected dust-producing planetesimals. In a planetary system with a belt of planetesimals (like the solar system's Kuiper Belt) and one or more interior giant planets, the trapping of dust particles in the mean motion resonances with the planets can create structure in the dust disk, as the particles accumulate at certain semimajor axes. Sufficiently massive planets may also scatter and eject dust particles out of a planetary system, creating a dust-depleted region inside the orbit of the planet. In anticipation of future observations of spatially unresolved debris disks with the Spitzer Space Telescope, we are interested in studying how the structure carved by planets affects the shape of the disk's spectral energy distribution (SED) and consequently whether the SED can be used to infer the presence of planets. We numerically calculate the equilibrium spatial density distributions and SEDs of dust disks originated by a belt of planetesimals in the presence of interior giant planets in different planetary configurations and for a representative sample of chemical compositions. The dynamical models are necessary to estimate the enhancement of particles near the mean motion resonances with the planets and to determine how many particles drift inside the planet's orbit. On the basis of the SEDs and predicted Spitzer colors we discuss what types of planetary systems can be distinguished and the main parameter degeneracies in the model SEDs.
Fueling the caries process: carbohydrate metabolism and gene regulation by Streptococcus mutans

The nature of the oral cavity and host behaviors has mandated that the oral microbiota evolve mechanisms for coping with environmental fluctuations, especially changes in the type and availability of carbohydrates. In the case of human dental caries, the presence of excess carbohydrates is often responsible for altering the local environment to be more favorable for species associated with the initiation and progression of disease, including Streptococcus mutans. Some of the earliest endeavors to understand how cariogenic species respond to environmental perturbations were carried out using chemostat cultivation, which provides fine control over culture conditions and bacterial behaviors. The development of genome-scale methodologies has allowed for the combination of sophisticated cultivation technologies with genome-level analysis to more thoroughly probe how bacterial pathogens respond to environmental stimuli. Recent investigations in S. mutans and other closely related streptococci have begun to reveal that carbohydrate metabolism can drastically impact pathogenic potential and highlight the important influence that nutrient acquisition has on the success of pathogens; inside and outside of the oral cavity. Collectively, research into pathogenic streptococci, which have evolved in close association with the human host, has begun to unveil the essential nature of careful orchestration of carbohydrate acquisition and catabolism to allow the organisms to persist and, when conditions allow, initiate or worsen disease.
Frequency of Germline Mutations in 25 Cancer Susceptibility Genes in a Sequential Series of Patients With Breast Cancer.

PURPOSE Testing for germline mutations in BRCA1/2 is standard for select patients with breast cancer to guide clinical management. Next-generation sequencing (NGS) allows testing for mutations in additional breast cancer predisposition genes. The frequency of germline mutations detected by using NGS has been reported in patients with breast cancer who were referred for BRCA1/2 testing or with triple-negative breast cancer. We assessed the frequency and predictors of mutations in 25 cancer predisposition genes, including BRCA1/2, in a sequential series of patients with breast cancer at an academic institution to examine the utility of genetic testing in this population. METHODS Patients with stages I to III breast cancer who were seen at a single cancer center between 2010 and 2012, and who agreed to participate in research DNA banking, were included (N = 488). Personal and family cancer histories were collected and germline DNA was sequenced with NGS to identify mutations. RESULTS Deleterious mutations were identified in 10.7% of women, including 6.1% in BRCA1/2 (5.1% in non-Ashkenazi Jewish patients) and 4.6% in other breast/ovarian cancer predisposition genes including CHEK2 (n = 10), ATM (n = 4), BRIP1 (n = 4), and one each in PALB2, PTEN, NBN, RAD51C, RAD51D, MSH6, and PMS2. Whereas young age (P < .01), Ashkenazi Jewish ancestry (P < .01), triple-negative breast cancer (P = .01), and family history of breast/ovarian cancer (P = .01) predicted for BRCA1/2 mutations, no factors predicted for mutations in other breast cancer predisposition genes. CONCLUSION Among sequential patients with breast cancer, 10.7% were found to have a germline mutation in a gene that predisposes women to breast or ovarian cancer, using a panel of 25 predisposition genes. Factors that predict for BRCA1/2 mutations do not predict for mutations in other breast/ovarian cancer susceptibility genes when these genes are analyzed as a single group. Additional cohorts will be helpful to define individuals at higher risk of carrying mutations in genes other than BRCA1/2.
Paclitaxel-loaded iron platinum stealth immunomicelles are potent MRI imaging agents that prevent prostate cancer growth in a PSMA-dependent manner

Background and methods: Problems with the clinical management of prostate cancer include the lack of both specific detection and efficient therapeutic intervention. We report the encapsulation of superparamagnetic iron platinum nanoparticles (SIPPs) and paclitaxel in a mixture of polyethyleneglycolated, fluorescent, and biotin-functionalized phospholipids to create multifunctional SIPP-PTX micelles (SPMs) that were conjugated to an antibody against prostate-specific membrane antigen (PSMA) for the specific targeting, magnetic resonance imaging (MRI), and treatment of human prostate cancer xenografts in mice. Results: SPMs were 45.4 ± 24.9 nm in diameter and composed of 160.7 ± 22.9 μg/mL iron, 247.0 ± 33.4 μg/mL platinum, and 702.6 ± 206.0 μg/mL paclitaxel. Drug release measurements showed that, at 37°C, half of the paclitaxel was released in 30.2 hours in serum and two times faster in saline. Binding assays suggested that PSMA-targeted SPMs specifically bound to C4-2 human prostate cancer cells in vitro and released paclitaxel into the cells. In vitro, paclitaxel was 2.2 and 1.6 times more cytotoxic than SPMs to C4-2 cells at 24 and 48 hours of incubation, respectively. After 72 hours of incubation, paclitaxel and SPMs were equally cytotoxic. SPMs had MRI transverse relaxivities of 389 ± 15.5 Hz/mM iron, and SIPP micelles with and without drug caused MRI contrast enhancement in vivo. Conclusion: Only PSMA-targeted SPMs and paclitaxel significantly prevented growth of C4-2 prostate cancer xenografts in nude mice. Furthermore, mice injected with PSMA-targeted SPMs showed significantly more paclitaxel and platinum in tumors, compared with nontargeted SPM-injected and paclitaxel-injected mice.
Probing Metal Defects in CCD Image Sensors

We have investigated the role of heavy metals in causing visible pixel defects in Charge Coupled Device (CCD) image sensors. Using a technique we call dark current spectroscopy, we can probe for deep-level traps in the active areas of completed image sensors with a sensitivity of 1 × 10 9 traps/cm 3 or better. Analysis of histograms of dark current images from these sensors shows that the presence of traps causes quantization in the dark current. Different metal traps have characteristic dark current generation rates that can identify the contaminant trap. By examining the temperature dependence of the dark current generation, we have calculated the energy levels and generation cross sections for gold, iron, nickel, and cobalt. Our results show the relationship of these traps to the “white spot” defects reported for image sensors.
STUDY ON THE ESTIMATION METHOD OF STRENGTH DEVELOPMENT OF CONCRETE UNDER VARIOUS MO ISTURE CURING CONDITIONS

コンクリート構造物が硬化後，所要の強度，耐久性，ひび割れ抵抗性等の性能を発揮するためには，硬化初期において適切に養生を行うことが重要である．本研究では，湿潤養生期間および給水養生の実施がコンクリートの性能改善に及ぼす効果を把握するために，普通ポルトランドセメントを用いたコンクリートを種々の湿潤養生条件下で養生し，圧縮強度発現特性に及ぼす影響を調査した．さらに，保水状態の差異がセメント鉱物の水和反応に及ぼす影響を定量的に評価し，水和生成物の生成量の観点から圧縮強度発現特性を評価した．その結果，保水状態がセメントの水和反応に及ぼす影響を考慮することで，種々の湿潤養生条件下での強度発現特性を評価可能であることを明らかとした．
18F-FDG PET/CT Is an Immediate Imaging Biomarker of Treatment Success After Liver Metastasis Ablation

The rationale of this study was to examine whether 18F-FDG PET/CT and contrast-enhanced CT performed immediately after percutaneous ablation of liver metastases are predictors of local treatment failure at 1 y. Methods: This Health Insurance Portability and Accountability Act–compliant, Institutional Review Board–approved retrospective study reviewed 25 PET/CT-guided thermal ablations performed from September 2011 to March 2013 on 21 patients (11 women and 10 men; mean age, 56.8 y; range, 35–79 y) for the treatment of liver metastases (colorectal, n = 23; breast, n = 1; and sarcoma, n = 1). One to 3 tumors (mean size, 2.3 cm; range, 0.7–4.6 cm; mean SUVmax, 22.7; range, 9.5–77.1) were ablated using radiofrequency (n = 16) or microwave (n = 9) energy in a single session. Immediate-postablation enhanced CT and PET/CT scans were qualitatively evaluated by 2 reviewers independently, and the results were compared with clinical and imaging outcome at 1 y. The PET/CT scans were also analyzed to determine tissue radioactivity concentration (TRC) from 3-dimensional regions of interest in the ablation zone, the margin, and the surrounding normal liver to calculate a TRC ratio, which was then compared with outcome at 1 y. Receiver operating characteristics (ROC) were used, and the maximal-accuracy threshold in predicting recurrence was calculated. Results: Eleven (44%) of the 25 tumors recurred within 1 y. Enhanced CT did not significantly correlate with recurrence (P = 0.288). Accuracy was 64% (16/25), and the area under the ROC curve was 0.601 (95% confidence interval [95% CI], 0.387–0.789). The accuracy of the qualitative analysis of 18F-FDG PET was 92% (23/25) (P < 0.001), and the area under the ROC curve was 0.929 (95% CI, 0.740–0.990). The mean TRC ratio was 40.6 in the recurrence group (SD, 9.2; range, 29.3–53.9) and 15.9 in the group without recurrence (SD, 7.3; range, 3–27.3). A TRC ratio of 28.3 predicted recurrence at 1 y with 100% accuracy (25/25) (P < 0.001), and the area under the ROC curve was 1 (95% CI, 0.863–1). Conclusion: Immediate PET/CT accurately predicts the success of liver metastasis ablation at 1 y and is superior to immediate enhanced CT.
Nursing practice, knowledge, attitudes and perceived barriers to evidence-based practice at an academic medical center.

AIM This paper is a report of a study to describe nurses' practices, knowledge, and attitudes related to evidence-based nursing, and the relation of perceived barriers to and facilitators of evidence-based practice. BACKGROUND Evidence-based practice has been recognized by the healthcare community as the gold standard for the provision of safe and compassionate healthcare. Barriers and facilitators for the adoption of evidence-based practice in nursing have been identified by researchers. Healthcare organizations have been challenged to foster an environment conducive to providing care based on evidence and not steeped in ritualized practice. METHODS A descriptive, cross-sectional research study was conducted in 2006-2007 with a convenience sample of 458 nurses at an academic medical center in California (response rate 44.68%). Two reliable and valid questionnaires were electronically formatted and administered using a secured website. Relationships between responses to the two instruments were examined and results compared with previously published data. RESULTS Organizational barriers (lack of time and lack of nursing autonomy) were the top perceived barriers. Facilitators were learning opportunities, culture building, and availability and simplicity of resources. Statistically significant correlations were found between barriers and practice, knowledge and attitudes related to evidence-based practice. CONCLUSION Similar barriers to the adoption of evidence-based practice have been identified internationally. Educators must work with managers to address organizational barriers and proactively support evidence-based practice.
From character to document representation with global context awareness

Bag-of-Words with TF-IDF or other weighting schemes is commonly adopted ways for document representation. However, they fail to capture sequential or semantic information in the sentence, and would lead to high-dimensional vector due to misspelling, acronyms and so on. Distributed word embedding and even document embedding methods are proposed to encode the semantic or contextual information. Whereas, the quality of the representation is not always good. To relieve the above mentioned problems, we propose a high-quality document representation model, which takes word morphology, semantic and sequential information of global context into consideration. The proposed model could outperform state-of-the-art traditional ways, word embedding-based and character-aware models on text classification task.
ECG Signal De-noising and Baseline Wander Correction Based on CEEMDAN and Wavelet Threshold

A novel electrocardiogram (ECG) signal de-noising and baseline wander correction method based on complete ensemble empirical mode decomposition with adaptive noise (CEEMDAN) and wavelet threshold is proposed. Although CEEMDAN is based on empirical mode decomposition (EMD), it represents a significant improvement of the original EMD by overcoming the mode-mixing problem. However, there has been no previous study on using CEEMDAN to de-noise ECG signals, to the authors’ best knowledge. In the proposed method, the original noisy ECG signal is decomposed into a series of intrinsic mode functions (IMFs) sorted from high to low frequency by CEEMDAN. Each IMF is then analyzed by the autocorrelation method to find out the first few high frequency IMFs containing random noise, and these IMFs should be de-noised by the wavelet threshold. The zero-crossing rate (ZCR) of all IMFs, including final residue, are computed, and the IMFs with ZCR less than a certain value are removed. Finally, the remaining IMFs are reconstructed to obtain the clean ECG signal. The proposed algorithm is validated through experiments using the MIT–BIH ECG databases, and the results show that the random noise in the ECG signal can be effectively suppressed, and at the same time the baseline wander can be corrected efficiently.
Can Performance on Daily Activities Discriminate Between Older Adults with Normal Cognitive Function and Those with Mild Cognitive Impairment?

A symposium, Pills and Ills: Methodologic Issues in Pharmacologic Research, was presented at the American Geriatrics Society Annual Scientific Meeting on May 4, 2013. The authors received support from National Institute on Aging Grants R01 AG037451, R01 AG027017, P30AG024827, T32AG021885, K07AG033174, R21AG045320; National Institute of Nursing Research Grant R01NR003178; Agency for Healthcare Research and Quality Grant R18HS020831; and Department of Veterans Affairs Health Services Research and Development Service Grant IIR 12–379. Conflict of Interest: None of the authors has relevant financial interests, activities, relationships, or affiliations, or other potential conflicts of interest to report. Author Contributions: Paper concept: Marcum, Gurwitz, Col on-Emeric, Hanlon. Manuscript: Marcum, Gurwitz, Col on-Emeric, Hanlon. Critical revision of manuscript for important intellectual content: Marcum, Gurwitz, Col on-Emeric, Hanlon. Sponsor’s Role: The sponsor of this research had no role or influence in matters relating to research design, methods, subject recruitment, data collection, analysis, or preparation of the paper.
Thermal Infrared Pedestrian Image Segmentation Using Level Set Method

The edge-based active contour model has been one of the most influential models in image segmentation, in which the level set method is usually used to minimize the active contour energy function and then find the desired contour. However, for infrared thermal pedestrian images, the traditional level set-based method that utilizes the gradient information as edge indicator function fails to provide the satisfactory boundary of the target. That is due to the poorly defined boundaries and the intensity inhomogeneity. Therefore, we propose a novel level set-based thermal infrared image segmentation method that is able to deal with the above problems. Specifically, we firstly explore the one-bit transform convolution kernel and define a soft mark, from which the target boundary is enhanced. Then we propose a weight function to adaptively adjust the intensity of the infrared image so as to reduce the intensity inhomogeneity. In the level set formulation, those processes can adaptively adjust the edge indicator function, from which the evolving curve will stop at the target boundary. We conduct the experiments on benchmark infrared pedestrian images and compare our introduced method with the state-of-the-art approaches to demonstrate the excellent performance of the proposed method.
Local chatter or international buzz? Language differences on posts about Zika research on Twitter and Facebook

Background When the Zika virus outbreak became a global health emergency in early 2016, the scientific community responded with an increased output of Zika-related research. This upsurge in research naturally made its way into academic journals along with editorials, news, and reports. However, it is not yet known how or whether these scholarly communications were distributed to the populations most affected by Zika. Methodology/Principal findings To understand how scientific outputs about Zika reached global and local audiences, we collected Tweets and Facebook posts that linked to Zika-related research in the first six months of 2016. Using a language detection algorithm, we found that up to 90% of Twitter and 76% of Facebook posts are in English. However, when none of the authors of the scholarly article are from English-speaking countries, posts on both social media are less likely to be in English. The effect is most pronounced on Facebook, where the likelihood of posting in English is between 11 and 16% lower when none of the authors are from English-speaking countries, as compared to when some or all are. Similarly, posts about papers written with a Brazilian author are 13% more likely to be in Portuguese on Facebook than when made on Twitter. Conclusions/Significance Our main conclusion is that scholarly communication on Twitter and Facebook of Zika-related research is dominated by English, despite Brazil being the epicenter of the Zika epidemic. This result suggests that scholarly findings about the Zika virus are unlikely to be distributed directly to relevant populations through these popular online mediums. Nevertheless, there are differences between platforms. Compared to Twitter, scholarly communication on Facebook is more likely to be in the language of an author’s country. The Zika outbreak provides a useful case-study for understanding how scientific outputs are communicated to relevant populations. Our results suggest that Facebook is a more effective channel than Twitter, if communication is desired to be in the native language of the affected country. Further research should explore how local media—such as governmental websites, newspapers and magazines, as well as television and radio—disseminate scholarly publication.
Leptomeningeal enhancement on preoperative brain MRI in patients with glioblastoma and its clinical impact

Leptomeningeal enhancement (LME) on preoperative brain magnetic resonance imaging (MRI) does not always indicate leptomeningeal seeding (LMS). With Stupp's regimen, authors have treated glioblastoma patients with LME on preoperative brain MRI but here we tried to find the clinical impact of LME.
A Reverse Genetics Platform That Spans the Zika Virus Family Tree

ABSTRACT Zika virus (ZIKV), a mosquito-borne flavivirus discovered in 1947, has only recently caused large outbreaks and emerged as a significant human pathogen. In 2015, ZIKV was detected in Brazil, and the resulting epidemic has spread throughout the Western Hemisphere. Severe complications from ZIKV infection include neurological disorders such as Guillain-Barré syndrome in adults and a variety of fetal abnormalities, including microcephaly, blindness, placental insufficiency, and fetal demise. There is an urgent need for tools and reagents to study the pathogenesis of epidemic ZIKV and for testing vaccines and antivirals. Using a reverse genetics platform, we generated six ZIKV infectious clones and derivative viruses representing diverse temporal and geographic origins. These include three versions of MR766, the prototype 1947 strain (with and without a glycosylation site in the envelope protein), and H/PF/2013, a 2013 human isolate from French Polynesia representative of the virus introduced to Brazil. In the course of synthesizing a clone of a circulating Brazilian strain, phylogenetic studies identified two distinct ZIKV clades in Brazil. We reconstructed viable clones of strains SPH2015 and BeH819015, representing ancestral members of each clade. We assessed recombinant virus replication, binding to monoclonal antibodies, and virulence in mice. This panel of molecular clones and recombinant virus isolates will enable targeted studies of viral determinants of pathogenesis, adaptation, and evolution, as well as the rational attenuation of contemporary outbreak strains to facilitate the design of vaccines and therapeutics. IMPORTANCE Viral emergence is a poorly understood process as evidenced by the sudden emergence of Zika virus in Latin America and the Caribbean. Malleable reagents that both predate and span an expanding epidemic are key to understanding the virologic determinants that regulate pathogenesis and transmission. We have generated representative cDNA molecular clones and recombinant viruses that span the known ZIKV family tree, including early Brazilian isolates. Recombinant viruses replicated efficiently in cell culture and were pathogenic in immunodeficient mice, providing a genetic platform for rational vaccine and therapeutic design. IMPORTANCE Viral emergence is a poorly understood process as evidenced by the sudden emergence of Zika virus in Latin America and the Caribbean. Malleable reagents that both predate and span an expanding epidemic are key to understanding the virologic determinants that regulate pathogenesis and transmission. We have generated representative cDNA molecular clones and recombinant viruses that span the known ZIKV family tree, including early Brazilian isolates. Recombinant viruses replicated efficiently in cell culture and were pathogenic in immunodeficient mice, providing a genetic platform for rational vaccine and therapeutic design.