bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adoption and utilization of NGS-based molecular profiling in community-based oncology practices: Insights from Sarah Cannon.
Authors: Burris III Howard A. , Schlauch Daniel , McKenzie Andrew , Sharma Yasha , Spigel David R. , Jones Suzanne Fields , Dilks Holli Hutcheson 
Published: October 2019

34 Background: The price of NGS-based sequencing technologies is falling, and the adoption of NGS-based testing is increasing in oncology practices. To date, a survey of the adoption and utilization of NGS-based technologies as a part routine oncology clinical care has not been performed. Thus, a comprehensive analysis of physician adoption and utilization of commercial NGS testing in the non-academic medical center, community-setting between 2012 and 2018 was performed. Methods: Medical Oncologists in the Sarah Cannon Research Institute network ordered commercially-available NGS-based molecular profiling for their patients as standard of care. Data use agreements were initiated between SCRI, affiliated medical oncology practices, and commercial NGS testing providers, and patient NGS data was subsequently analyzed starting in 2012. Results: Community-based NGS testing rates with the Sarah Cannon network were 5.75/month in 2012 and 440/month in 2018. Plasma-based NGS testing began in 2014 and comprised 4.9% of total testing compared to 40.1% in 2018. The number of oncologist ordering molecular profiles increased from 11 in 2012 to 269 in 2018. Physician test utilization grew from an average of 6 tests/physician to 22 tests/physician in 2012 and 2018, respectively. NGS tests were performed on 34 different tumor types and biopsies were taken from both primary tumors (~40%) and metastatic sites (~60%). Tissue-based tests averaged 14 mutations/sample while plasma-based tests averaged 4 mutations/sample. There was a 74% decrease in median time between biopsy collection and NGS test results between 2012 and 2018 (131 and 34 days, respectively), indicating a shift toward the use of fresh – non-archival – tissue in recent years. Conclusions: These data establish NGS-based testing trends in community oncology practices and show that NGS-based tumor testing utilization has increased in the community-setting between 2012 and 2018. NGS testing is performed on a wide array of tumor types and oncologists order tests earlier and utilize fresher biopsies.
A single-cell atlas of hepatocellular carcinoma.
Authors: Sharma Ankur 
Published: October 2019

46 Background: Tumors reside and evolve in a complex ecosystem of immune and non-immune stromal cells. Methods: We employed multi-sectoral single-cell RNA-seq to catalogue intra-tumor heterogeneity in human hepatocellular carcinoma (HCC). Results: We generated single-cell atlas of ~76,000 cells from fourteen HCC patients, each consisting of 2-5 tumor and matched adjacent normal sectors. In total, we profiled 57 individual tumor and normal sectors consisting of HBV+ and HBV- HCC. By analysing matched normal and malignant sectors we observed intriguing remodelling of the tumor microenvironment (TME).We identify >70 distinct cells-states in HCC including novel, previously uncharacterized subpopulations. Specifically, we demonstrate remarkable heterogeneity in hepatocytes, fibroblast and endothelial cells. Most importantly, we consistently observed a marked remodellingof stromal cells suggesting a role in dynamic tumor-TME interactions. Conclusions: We present the first comprehensive single-cell atlas of HCC. This resource provides unprecedented insights into liver cancer, which will pave the way for early detection and therapeutic targeting.
A phase 1, open-label, multicenter study to assess the safety, tolerability, and immunogenicity of mRNA-4157 alone in subjects with resected solid tumors and in combination with pembrolizumab in subjects with unresectable solid tumors (Keynote-603).
Authors: Burris III Howard A. , Patel Manish R. , Cho Daniel C. , Clarke Jeffrey Melson , Gutierrez Martin , Zaks Tal Z. , Frederick Joshua , Hopson Kristen , Mody Kinjal , Binanti-Berube Alverina , Robert-Tissot Celine , Cowens Kristen , Breton Ben , Zhong Shan , Zhou Honghong , Cohen Pamela Sarah , Keating Karen , Meehan Robert S. , Gainor Justin F. 
Published: October 2019

93 Background: T-cell targeting of mutation-derived epitopes (neoantigens) has been demonstrated to drive anti-tumor responses. Immunizing patients against such neoantigens in combination with a checkpoint inhibitor (CPI) may elicit greater anti-tumor responses than CPI alone. Mutations are rarely shared between patients, thus requiring a personalized approach to vaccine design. Methods: This is an interim report of a phase I dose escalation study of mRNA-4157 given as monotherapy in patients with resected solid tumors and in combination with pembrolizumab in patients with unresectable solid tumors. mRNA-4157 is a lipid encapsulated personalized vaccine encoding multiple neoantigens selected using a proprietary algorithm designed to induce neoantigen specific T cells and associated anti-tumor responses. Patients received up to 9 cycles (Q3W) of mRNA-4157 by IM injection (0.04 – 1 mg). In combination arm, pembrolizumab (200 mg) was administered for two cycles prior to combination with mRNA-4157 for up to 9 cycles and may continue on pembrolizumab monotherapy for up to 2 years. Results: As of 10-May-2019, 33 patients received mRNA-4157 alone or in combination. No DLTs or related SAEs or AEs ≥ grade 3 were reported. Of the 13 patients treated with monotherapy (3 melanoma, 8 NSCLC, 2 MSI-high CRC), 11 patients remain disease free on study, median follow-up of 10 months. Of the 20 patients treated in combination (1 TMB-high metastatic cutaneous squamous cell, 4 bladder, 2 HNSCC, 1 melanoma, 7 NSCLC, 2 SCLC, 3 MSI-high (CRC, prostate, endometrial), 13 had received prior CPI, 5 PRs (2 in patients previously treated with PD-1/L1 inhibitors), 6 SD, and 8 PD were reported. Neoantigen specific CD8+ T-cell responses have been detected. Conclusions: mRNA-4157 is safe and well tolerated at all dose levels tested. Clinical responses have been observed in combination with pembrolizumab and neoantigen-specific T cells have been induced, supporting the advancement of mRNA-4157 to phase 2. Clinical trial information: NCT 03739931.
Treatment-Induced Neuropathy of Diabetes (TIND) in Pediatrics: A Case Report and Review of the Literature
Authors: Chandler Erika , Brown Martin , Wintergerst Kupper , Doll Elizabeth 
Published: October 2019

Abstract

Context
Treatment-induced neuropathy of diabetes (TIND) is a rarely reported but important consideration in patients presenting with an acute onset of neuropathic symptoms following rapid correction of hyperglycemia in diabetes. Although it has been reported in children, the preponderance of literature focuses on adults with TIND.

Case Description
We report an 18-year-old male with this condition and his clinical course. We then discuss the proposed pathophysiology of TIND and review the literature. We also provide a standard workup for the diagnosis of TIND.

Conclusion
In both pediatric and adult populations, TIND should be considered in diabetic patients who develop neuropathy acutely following rapid correction of hyperglycemia. Because the pathophysiology of TIND remains poorly understood, there is insufficient information regarding how to target susceptible individuals and prevent the development of TIND.
Data Analytics, Innovation, and Firm Productivity
Authors: Wu Lynn , Hitt Lorin , Lou Bowen 
Published: October 2019

We examine the relationship between data analytics capabilities and innovation using detailed firm-level data. To measure innovation, we first utilize a survey to capture two types of firm practices, process improvement and new technology development for 331 firms. We then use patent data to further analyze new technology development for a broader sample of more than 2,000 publicly traded firms. We find that data analytics capabilities are more likely to be present and are more valuable in firms that are oriented around process improvement and that create new technologies by combining a diverse set of existing technologies than they are in firms that are focused on generating entirely new technologies. These results are consistent with the theory that data analytics are complementary to certain types of innovation because they enable firms to expand the search space of existing knowledge to combine into new technologies, as well as the theoretical arguments that data analytics support incremental process improvements. Data analytics appears less effective for developing entirely new technologies or creating combinations involving a few areas of knowledge, innovative approaches where there is either limited data or limited value in integrating diverse knowledge. Overall, our results suggest that firms that have historically focused on specific types of innovation—process innovation and innovation by diverse recombination—may receive the most benefits from using data analytics.This paper was accepted by Chris Forman, information systems.
Advance Service Reservations with Heterogeneous Customers
Authors: Stein Clifford , Truong Van-Anh , Wang Xinshang 
Published: October 2019

We study a fundamental model of resource allocation in which a finite number of resources must be assigned in an online manner to a heterogeneous stream of customers. The customers arrive randomly over time according to known stochastic processes. Each customer requires a specific amount of capacity and has a specific preference for each of the resources with some resources being feasible for the customer and some not. The system must find a feasible assignment of each customer to a resource or must reject the customer. The aim is to maximize the total expected capacity utilization of the resources over the horizon. This model has application in services, freight transportation, and online advertising. We present online algorithms with bounded competitive ratios relative to an optimal off-line algorithm that knows all stochastic information. Our algorithms perform extremely well compared with common heuristics as demonstrated on a real data set from a large hospital system in New York City. This paper was accepted by Yinyu Ye, optimization.
The Use of PSPP Software in Learning Statistics
Authors: Sto.-Tomas Minerva , Tindowen Darin Jan , Mendezabal Marie Jean , Quilang Pyrene , Agustin Erovita Teresita 
Published: October 2019

<p style="text-align:justify">This descriptive and correlational study investigated the effects of using PSPP in learning Statistics on students’ attitudes and performance. The respondents of the study were 200 Grade 11 Senior High School students who were enrolled in Probability and Statistics subject during the Second Semester of School Year 2018-2019. The respondents were randomly selected from those classes across the different academic strands that used PSPP in their Probability and Statistics subject through stratified random sampling. The results revealed that the students have favorable attitudes towards learning Statistics with the use of the PSPP software. The students became more interested and engaged in their learning of statistics which resulted to an improved academic performance.</p>
Mobility and distribution of whey solutions in soil columns
Authors: Silva Nara Cristina de Lima , Ruiz Hugo Alberto , Almeida Leandro da Silva 
Published: October 2019

In Brazil’s food industry, dairy production is one of the most important sectors, whose most relevant byproduct is whey. Due to the difficulties of reuse and environmental impacts caused when discarded as effluent in water bodies, an alternative for its final destination would be the application of this residue in the soil. The purpose of this study was to determine chemical changes and mobility and distribution of solutes in the soil after applications of whey rates, as well as to analyze the leachate collected after each application. The test was carried out in a laboratory, in PVC columns filled with soil. The treatments consisted of 2 x 2 samples of a typical dystrophic Red-Yellow Oxisol (Oxisol) and a typical dystrophic fluvic Inceptisol (Inceptisol), sampled in the layers 0- 20 and 20-40 cm. Each experimental unit consisted of 11 PVC rings (diameter of 6.6 cm, height of 7 cm). The columns were arranged in a randomized complete block design with five replications. Four whey rates were applied, corresponding to a soil pore volume of 0.2, at intervals of six days. The leachate was collected 24 and 120 hours after each application to measure pH, electrical conductivity (EC), chemical oxygen demand (COD), contents of total N, N-NH4+, N-NO3-, Na, K, Ca, and Mg. Six days after the last whey application, the columns were opened and the soil of each ring was analyzed for pH, EC, total N, N-NH4+, N-NO3-, Na, K, Ca, and Mg. The high electrolyte concentrations of whey resulted in a general increase in soil EC. The increase of N-NH4+ and N-NO3- in the soil was high due to mineralization. High concentrations of K, Na and Ca caused displacement of Mg from the exchange complex. It was concluded that from an environmental standpoint, whey soil application is a viable alternative, given that problems of salinization and leaching of undesirable elements are avoided by an adequate management.
Mesenchymal stem cell-derived exosomes improve diabetes mellitus-induced myocardial injury and fibrosis via inhibition of TGF-Î²1/Smad2 signaling pathway
Authors: Lin Yuan , Zhang Fang , Lian Xiao-fen , Peng Wei-qun , Yin Chao-yao 
Published: October 2019

The aim of this study is to investigate the effect of mesenchymal stem cell (MSC)-derived exosomes on diabetes mellitus-induced myocardial injury, and the underlying mechanism. Thirty adult male Sprague Dawley rats were randomly assigned to three groups of ten rats each: normal control group, diabetic control group and MSC exosomes group. Exosomes were isolated from MSCs through gradient ultracentrifugation. With the exception of normal control, diabetes mellitus (DM) was induced in the rats with a single intraperitoneal injection of 30 mg/kg body weight streptozotocin (STZ) in 0.1 mol/L sodium citrate buffer. Rats in MSC exosomes group were intravenously injected with MSC-derived exosomes once a week for 12 weeks. Left ventricular collagen (LVC) level was measured using acid hydrolysis method. Fatty acid transporters (FATPs) and fatty acid beta oxidase (FA-Î²-oxidase) were determined using enzyme-linked immunosorbent assay (ELISA). Gene and protein expressions of TGF-Î² and Smad2 were determined using real-time quantitative polymerase chain reaction (qRT-PCR) and Western blotting. Flow cytometric analysis and Western blotting revealed positive expression of exosomal specific marker, CD63. The level of LVC was significantly higher in diabetic control group than in normal control group, but was significantly reduced after treatment with MSC-derived exosomes (p < 0.05). The levels of FATPs and FA-Î²-oxidase were significantly lower in diabetic control group than in normal control group (p < 0.05). However, treatment with MSC-derived exosomes significantly increased the levels of these proteins (p < 0.05). The levels of expression of TGF-Î²1 and Smad2 mRNAs were significantly higher in the diabetic control group than in normal control group, but were significantly reduced after treatment with MSC-derived exosomes (p < 0.05). The expressions of TGF-Î²1 and Smad2 proteins were also significantly upregulated in diabetic control group, when compared with normal control group (p < 0.05). However, treatment with MSC-derived exosomes significantly down-regulated the expression of these proteins (p < 0.05). The results obtained in this study indicate that MSC-derived exosomes improve DM-induced myocardial injury and fibrosis via inhibition of TGF-Î²1/Smad2 signaling pathway.
Regulation of signaling pathways by Ampelopsin (Dihydromyricetin) in different cancers: exploring the highways and byways less travelled
Authors: Fayyaz Sundas , Qureshi Muhammad Zahid , Alhewairini Saleh S , Avnioglu Seda , Attar Rukset , Sabitaliyevich Uteuliyev Yerzhan , Buha Aleksandra , Salahuddin Hina , Adylova Aima , Tahir Fatima , Pawlak-Adamska Edyta 
Published: October 2019

Ampelopsin or Dihydromyricetin is gradually emerging as a high-quality natural product because of its ability to modulate wide-ranging signaling pathways. Ampelopsin (Dihydromyricetin) has been reported to effectively modulate growth factor receptor (VEGFR2 and PDGFRÎ²) mediated signaling, TRAIL/TRAIL-R pathway, JAK/STAT and mTOR-driven signaling in different cancers. Ampelopsin (Dihydromyricetin) has also been shown to exert inhibitory effects on the versatile regulators which trigger EMT (Epithelial-to-Mesenchymal Transition). Findings obtained from in-vitro studies are encouraging and there is a need to comprehensively analyze how Ampelopsin (Dihydromyricetin) inhibits tumor growth in different cancer models. Better knowledge of efficacy of Ampelopsin (Dihydromyricetin) in tumor bearing mice will be helpful in maximizing its translational potential.
Ensemble Algorithm for Parametrized Flow Problems with Energy Stable Open Boundary Conditions
Authors: Takhirov Aziz , Waters Jiajia 
Published: October 2019

Abstract
We propose novel ensemble calculation methods for Navier–Stokes equations subject to various
initial conditions, forcing terms and viscosity coefficients.
We establish the stability of the schemes under a CFL condition involving velocity fluctuations. Similar to related works, the
schemes require solution of a single system with multiple right-hand sides.
Moreover, we extend the ensemble calculation method to problems with open boundary conditions, with provable energy stability.
A New Method of Estimating the Process Capability Index with Exponential Distribution Using Interval Estimate of the Parameter
Authors: Vedururu Sai Sarada , Subbarayudu M. , Sarma K. V. S. 
Published: October 2019

Abstract
This paper deals with a new method of deriving the Process Capability Index (PCI) when the quality characteristic X follows a positively skewed distribution. The focus of the paper is to derive a new estimate of PCI by taking into account the

{100(1-{\alpha})}

Confidence Intervals (CI) of the parameter (s) and arriving at a new expression. The formula

{{C}_{{s}}}

, proposed by Wright (1995) which contains a component for skewness, is reexamined and a new estimate is constructed by utilizing the lower, middle and upper values of the CI of the parameter. The weighted average of the three possible estimates of

{{C}_{{s}}}

is proposed as the new estimate by taking the weights inversely proportional to the squared deviation from the hypothetical value of

{{C}_{{s}}}

. The properties of the estimate are studied by simulation using one parameter exponential distribution.
Randomized nonlinear software-oriented MDS diffusion layers
Authors: Mirzaee Shamsabad Mohammad Reza , Dehnavi Seyed Mojtaba , Mahmoodi Rishakani Akbar 
Published: October 2019

Abstract
MDS diffusion layers are critical components in the design of symmetric ciphers.
In this paper, after introducing some new algebraic structures, we provide new MDS matrices over special types of R-modules.
With the help of the proposed methodology, we have more flexibility in designing software-oriented diffusion layers.
Most notably, we construct randomized and/or nonlinear MDS diffusion layers, based upon the presented theoretical results, and discuss the resistance of the presented diffusion layers against various kinds of cryptanalysis, compared with classical linear diffusion layers.
Oscillation of first-order differential equations with several non-monotone retarded arguments
Authors: Bereketoglu Huseyin , Karakoc Fatma , Oztepe Gizem S. , Stavroulakis Ioannis P. 
Published: October 2019

AbstractConsider the first-order linear differential equation with several non-monotone retarded argumentsx′⁢(t)+∑i=1mpi⁢(t)⁢x⁢(τi⁢(t))=0{x^{\prime}(t)+\sum_{i=1}^{m}p_{i}(t)x(\tau_{i}(t))=0},t≥t0{t\geq t_{0}}, where the functionspi,τi∈C⁢([t0,∞),ℝ+){p_{i},\tau_{i}\in C([t_{0},\infty),\mathbb{R}^{+})}, for everyi=1,2,…,m{i=1,2,\ldots,m},τi⁢(t)≤t{\tau_{i}(t)\leq t}fort≥t0{t\geq t_{0}}andlimt→∞⁡τi⁢(t)=∞{\lim_{t\to\infty}\tau_{i}(t)=\infty}. New oscillation criteria which essentially improve the known results in the literature are established. An example illustrating the results is given.
The development and psychometric evaluation of a new instrument to market healthy breakfast and snacks among adolescents
Authors: Bastami Fatemeh , Zamani-Alavijeh Fereshteh , Mostafavi Firoozeh 
Published: October 2019

Abstract

Background
The consumption of non-nutritious snacks instead of a proper breakfast is becoming more widespread among adolescents. It is expected that using the 4P (product, price, place, promotion) strategies of the social marketing (SM) model can help to better identify factors affecting healthy breakfast and snack consumption. The objective of this study was to develop and evaluate the psychometric properties of the Healthy Breakfast and Snack Consumption Scale (HBSCS) using the SM model.

Methods
This was a cross-sectional descriptive study that was conducted in 2017. First, a scale was developed using the results of a qualitative research based on the SM model. Then, its face, content and construct validities as well as its reliability were assessed. Construct validity was evaluated via exploratory factor analysis conducted on a random sample of 300 high school pupils selected from five girls’ schools located in Isfahan, Iran, using the multistage cluster sampling method. Exploratory factor analysis was performed using the methods of principle components extraction and varimax rotation with eigenvalues greater than 1.

Results
A four-factor structure that explained 61.73% of the total variance of the HBSCS included healthy breakfast and snack preferences, readiness to pay the price, place preferences and communication channel preferences. Items with an impact score of less than 1.5 were removed. Additionally, items with content validity ratio values of less than 0.62 and content validity index values of less than 0.79 were deleted. The Kaiser-Meyer-Olkin measure value was 0.74 [chi-squared (χ2) = 2353.622; p-value < 0.001]. The Cronbach’s α values of the scale and its four dimensions were 0.71 and 0.56–0.72, respectively.

Conclusion
This scale has acceptable validity and reliability. School authorities and health professionals can use this scale to screen adolescents at risk of consuming unhealthy foods and snacks. Besides, the scale might be used as a framework for assessing, implementing and promoting healthy eating behaviors among pupils.
The enclosure method for inverse obstacle scattering over a finite time interval: VI. Using shell-type initial data
Authors: Ikehata Masaru 
Published: October 2019

Abstract
A simple idea of finding a domain that encloses an unknown discontinuity embedded in a body
is introduced by considering an inverse boundary value problem for the heat equation.
The idea gives a design of a special heat flux on the surface of the body such that from
the corresponding temperature field on the surface one can extract the smallest radius of
the sphere centered at an arbitrary given point in the whole space and enclosing unknown inclusions.
Unlike before, the designed flux is free from a large parameter. An application of the idea
to a coupled system of the elastic wave and heat equations are also given.