bluuebunny/crossref_metadata_2025_split huggingface dataset:
Graph embedding algorithms for attributed and temporal graphs
Authors: Goyal Palash 
Published: May 2020

Palash Goyal is a Senior Research Scientist at Samsung Research America. In 2019, he got his doctoral degree in Computer Science from University of Southern California under the advisory of Dr. Emilio Ferrara. Over the course of his PhD, he worked with several government funded projects including IARPA and DARPA spanning domains of time series prediction, text analysis and understanding social behavior. He also applied his work on graph embedding in various industrial settings including developing automation systems in Siemens Corporate, identifying key steam injection candidate oil wells for Chevron and developing recommendation system for Target. His work on tracking temporal evolution of graphs using non-timestamped data was nominated for best paper award in ACM Hypertext.
In his thesis, supervised by Dr. Emilio Ferrara (USC Information Sciences Institute), he ex- tended the work of learning low-dimensional representations of nodes in a graph in several di- rections. Firstly, he published a survey of existing graph embedding approaches and shed light into the dependency between them drawing insights into the relations effectively captured by the methods. He further proposed a benchmark to evaluate any graph embedding approach and un- derstand its applicability. Secondly, he built models to capture temporal patterns in sequential graphs and efficiently update embeddings for streaming graphs. Finally, he developed multi-modal models for learning representations through graph data as well as other forms of data available for the nodes and edges including text.
How spelling reform would promote better writing and speaking
Authors: Yaffe Philip 
Published: May 2020

Each "Communication Corner" essay is self-contained; however, they build on each other. For best results, before reading this essay and doing the exercise, go to the first essay "How an Ugly Duckling Became a Swan," then read each succeeding essay.
Instead of mastering the chaos of learning to read and write in English, perhaps we should start spelling things the way they sound.
Senescent Stromal Cells Promote Cancer Resistance through SIRT1 Loss-Potentiated Overproduction of Small Extracellular Vesicles
Authors: Han Liu , Long Qilai , Li Shenjun , Xu Qixia , Zhang Boyi , Dou Xuefeng , Qian Min , Jiramongkol Yannasittha , Guo Jianming , Cao Liu , Chin Y. Eugene , Lam Eric W.-F. , Jiang Jing , Sun Yu 
Published: May 2020

Abstract

Cellular senescence is a potent tumor-suppressive program that prevents neoplastic events. Paradoxically, senescent cells develop an inflammatory secretome, termed the senescence-associated secretory phenotype, which is implicated in age-related pathologies including cancer. Here, we report that senescent cells actively synthesize and release small extracellular vesicles (sEV) with a distinctive size distribution. Mechanistically, SIRT1 loss supported accelerated sEV production despite enhanced proteome-wide ubiquitination, a process correlated with ATP6V1A downregulation and defective lysosomal acidification. Once released, senescent stromal sEVs significantly altered the expression profile of recipient cancer cells and enhanced their aggressiveness, specifically drug resistance mediated by expression of ATP-binding cassette subfamily B member 4 (ABCB4). Targeting SIRT1 with agonist SRT2104 prevented development of cancer resistance by restraining sEV production by senescent stromal cells. In clinical oncology, sEVs in peripheral blood of posttreatment cancer patients were readily detectable by routine biotechniques, presenting an exploitable biomarker to monitor therapeutic efficacy and predict long-term outcome. Together, this study identifies a distinct mechanism supporting pathologic activities of senescent cells and provides a potent avenue to circumvent advanced human malignancies by cotargeting cancer cells and their surrounding microenvironment, which contributes to drug resistance via secretion of sEVs from senescent stromal cells.

Significance:
Senescent stromal cells produce a large number of sEVs to promote cancer resistance in therapeutic settings, a process driven by SIRT1 decline in stromal cells and ABCB4 augmentation in cancer cells.
See related commentary by Wiley, p. 3193
Immunotherapeutic Response in Tumors Is Affected by Microenvironmental ROS
Authors: Hayward Simon W. 
Published: May 2020

Abstract
Carcinoma-associated fibroblasts (CAF) are a potential therapeutic target for both direct and indirect regulation of cancer progression and therapy response. In this issue of Cancer Research, Ford and colleagues investigate the influence of CAF on the immune environment of tumors, specifically focusing on the regulation of CD8+ T cells, required for immune therapy response. Their work suggests a role for stromally expressed NADPH oxidase 4 (NOX4) as a modulator of reactive oxygen species that in turn can reduce the number of CD8+ T cells locally. Inhibition of NOX4 increased CD8+ T cells and restored responsiveness to immune therapy, suggesting an indirect stromally targeted avenue for therapy resensitization.
See related article by Ford et al., p. 1846
Radiation Attenuates Prostate Tumor Antiviral Responses to Vesicular Stomatitis Virus Containing IFNβ, Resulting in Pronounced Antitumor Systemic Immune Responses
Authors: Udayakumar Thirupandiyur S. , Betancourt Dillon M. , Ahmad Anis , Tao Wensi , Totiger Tulasigeri M. , Patel Mausam , Marples Brian , Barber Glen , Pollack Alan 
Published: May 2020

Abstract

Vesicular stomatitis virus (VSV) expressing IFNβ induces apoptosis in multiple tumor models while maintaining an excellent safety profile. VSV-IFNβ is oncoselective due to permissive replication in cells with an altered IFN pathway. The human VSV-IFNβ (hIFNβ) vector is currently used in clinical trials as a standalone therapy; however, we hypothesized that oncolytic virotherapy might be more effective when used in combination with radiotherapy (RT). We investigated the synergistic effects of RT and VSV-hIFNβ in the subcutaneous PC3 and orthotopic LNCaP prostate xenograft models and a syngeneic RM9 prostate tumor model. VSV-IFNβ combined with RT amplified tumor killing for PC3 and LNCaP xenografts, and RM9 tumors. This was attributed to the induction of proapoptotic genes leading to increased VSV-IFNβ infection and replication, VSV expression, and oncolysis. In the RM9 tumors, combination therapy resulted in a robust antitumor immune response. Treated RM9 tumor-bearing mice demonstrated an increase in CD8+ and CD4+ T-cell numbers, 100% resistance to tumor rechallenge, and reduced resistance to reimplantation challenge with CD8+ knockdown. RT enhanced the activity of VSV-mediated oncolysis via attenuation of the innate antiviral response, resulting in increased VSV replication and the generation of an adaptive immune response earmarked by an increase in CD8+ lymphocyte numbers and antitumor activity. Local tumor irradiation combined with VSV-IFNβ affects tumor cell death through direct and systemic activity in conjunction with pronounced antitumor immunity.

Implications:
Radiotherapy enhances VSV-mediated oncolysis and anti-tumor immunity, indicating that the ombination has promise for very high risk prostate cancer.
Apolipoprotein C2 - CD36 Promotes Leukemia Growth and Presents a Targetable Axis in Acute Myeloid Leukemia
Authors: Zhang Tian , Yang Jiawen , Vaikari Vijaya P. , Beckford John S. , Wu Sharon , Akhtari Mojtaba , Alachkar Houda 
Published: May 2020

Abstract

Acute myeloid leukemia (AML) is a devastating hematologic malignancy that affects the hematopoietic stem cells. The 5-year overall survival (OS) of patients with AML is less than 30%, highlighting the urgent need to identify new therapeutic targets. Here, we analyze gene expression datasets for genes that are differentially overexpressed in AML cells compared with healthy hematopoietic cells. We report that apolipoprotein C2 (APOC2) mRNA is significantly overexpressed in AML, particularly in patients with mixed-lineage leukemia rearrangements. By multivariate analysis, high APOC2 expression in leukemia blasts is significantly associated with decreased OS (HR: 2.51; 95% CI, 1.03–6.07; P = 0.04). APOC2 is a small secreted apolipoprotein that constitutes chylomicrons, very-low-density lipoproteins, and high-density lipoproteins with other apolipoproteins. APOC2 activates lipoprotein lipase and contributes to lipid metabolism. By gain and loss of function approaches in cultured AML cells, we demonstrate that APOC2 promotes leukemia growth via CD36-mediated LYN–ERK signaling activation. Knockdown or pharmacological inhibition of either APOC2 or CD36 reduces cell proliferation, induces apoptosis in vitro, and delays leukemia progression in mice. Altogether, this study establishes APOC2–CD36 axis as a potential therapeutic target in AML.

Significance:
The majority of patients with AML die within five years of diagnosis. We reveal that lipid transporter APOC2 is elevated in AML and promotes leukemic cell metabolism and growth via CD36, and provide preclinical evidence that targeting this pathway may be beneficial in AML.
This article is highlighted in the In This Issue feature, p. 127
Effects of Liraglutide on Worsening Renal Function Among Patients With Heart Failure With Reduced Ejection Fraction
Authors: Redouane Brahim , Greene Stephen J. , Fudim Marat , Vaduganathan Muthiah , Ambrosy Andrew P. , Sun Jie-Lena , DeVore Adam D. , McNulty Steven E. , Mentz Robert J. , Hernandez Adrian F. , Felker G. Michael , Cooper Lauren B. , Borlaug Barry A. , Velazquez Eric J. , Margulies Kenneth B. , Sharma Abhinav 
Published: May 2020

Background:
The FIGHT (Functional Impact of GLP-1 [glucagon-like peptide-1] for Heart Failure Treatment) trial randomized 300 patients with heart failure with reduced ejection fraction (HFrEF) and a recent hospitalization for heart failure to liraglutide versus placebo. While there was no difference in the primary outcome (rank score of time to death, time to rehospitalization for heart failure, and change in NT-proBNP [N-terminal pro-B-type natriuretic peptide]), there was a significant increase in cystatin C among patients randomized to liraglutide raising concern of adverse renal outcomes. We performed a post hoc analysis of FIGHT to investigate whether liraglutide was associated with worsening renal function (WRF).

Methods:
The relationship between randomization to liraglutide and WRF was evaluated using logistic regression models. Two hundred seventy-four patients (91%) had complete data to assess for WRF defined as: increase in SCr ≥0.3 mg/dL, or ≥25% decrease in estimated glomerular filtration rate, or an increase in cystatin C ≥0.3 mg/L from baseline to 180-days.

Results:
Patients with WRF (n=113, 41%), compared with those without, were older, had more comorbidities, and lower utilization of guideline-directed medical treatment. Logistic regression models showed that age and baseline cystatin C levels were associated with WRF. In adjusted models, liraglutide was not associated with excess risk of WRF compared with placebo (odds ratio, 1.02 [95% CI, 0.62–1.67]). There was also no difference in the rank score when WRF was added as a fourth-tier outcome.

Conclusions:
Liraglutide was not associated with WRF among patients with HFrEF and a recent hospitalization for heart failure. These data support the relative renal safety profile of liraglutide among patients with HFrEF.

Registration:

URL:
http://www.clinicaltrials.gov
. Unique identifier: NCT01800968.
West Coast Forecast Challenges and Development of Atmospheric River Reconnaissance
Authors: Ralph F. Martin , Cannon Forest , Tallapragada Vijay , Davis Christopher A. , Doyle James D. , Pappenberger Florian , Subramanian Aneesh , Wilson Anna M. , Lavers David A. , Reynolds Carolyn A. , Haase Jennifer S. , Centurioni Luca , Ingleby Bruce , Rutz Jonathan J. , Cordeira Jason M. , Zheng Minghua , Hecht Chad , Kawzenuk Brian , Delle Monache Luca 
Published: May 2020

AbstractWater management and flood control are major challenges in the western United States. They are heavily influenced by atmospheric river (AR) storms that produce both beneficial water supply and hazards; for example, 84% of all flood damages in the West (up to 99% in key areas) are associated with ARs. However, AR landfall forecast position errors can exceed 200 km at even 1-day lead time and yet many watersheds are <100 km across, which contributes to issues such as the 2017 Oroville Dam spillway incident and regularly to large flood forecast errors. Combined with the rise of wildfires and deadly post-wildfire debris flows, such as Montecito (2018), the need for better AR forecasts is urgent. Atmospheric River Reconnaissance (AR Recon) was developed as a research and operations partnership to address these needs. It combines new observations, modeling, data assimilation, and forecast verification methods to improve the science and predictions of landfalling ARs. ARs over the northeast Pacific are measured using dropsondes from up to three aircraft simultaneously. Additionally, airborne radio occultation is being tested, and drifting buoys with pressure sensors are deployed. AR targeting and data collection methods have been developed, assimilation and forecast impact experiments are ongoing, and better understanding of AR dynamics is emerging. AR Recon is led by the Center for Western Weather and Water Extremes and NWS/NCEP. The effort’s core partners include the U.S. Navy, U.S. Air Force, NCAR, ECMWF, and multiple academic institutions. AR Recon is included in the “National Winter Season Operations Plan” to support improved outcomes for emergency preparedness and water management in the West.
Path Properties of Atmospheric Transitions: Illustration with a Low-Order Sudden Stratospheric Warming Model
Authors: Finkel Justin , Abbot Dorian S. , Weare Jonathan 
Published: May 2020

AbstractMany rare weather events, including hurricanes, droughts, and floods, dramatically impact human life. To accurately forecast these events and characterize their climatology requires specialized mathematical techniques to fully leverage the limited data that are available. Here we describe transition path theory (TPT), a framework originally developed for molecular simulation, and argue that it is a useful paradigm for developing mechanistic understanding of rare climate events. TPT provides a method to calculate statistical properties of the paths into the event. As an initial demonstration of the utility of TPT, we analyze a low-order model of sudden stratospheric warming (SSW), a dramatic disturbance to the polar vortex that can induce extreme cold spells at the surface in the midlatitudes. SSW events pose a major challenge for seasonal weather prediction because of their rapid, complex onset and development. Climate models struggle to capture the long-term statistics of SSW, owing to their diversity and intermittent nature. We use a stochastically forced Holton–Mass-type model with two stable states, corresponding to radiative equilibrium and a vacillating SSW-like regime. In this stochastic bistable setting, from certain probabilistic forecasts TPT facilitates estimation of dominant transition pathways and return times of transitions. These “dynamical statistics” are obtained by solving partial differential equations in the model’s phase space. With future application to more complex models, TPT and its constituent quantities promise to improve the predictability of extreme weather events through both generation and principled evaluation of forecasts.
Tracing Future Spring and Summer Drying in Southern Africa to Tropical Lows and the Congo Air Boundary
Authors: Howard Emma , Washington Richard 
Published: May 2020

AbstractIn southern Africa, models from phase 5 of the Coupled Model Intercomparison Project (CMIP5) predict robust future drying associated with a delayed rainy-season onset in the austral spring and a range of wetting and drying patterns in the austral summer. This paper relates these rainfall changes to dynamical shifts in two classes of weather systems: the Congo Air Boundary (CAB) and tropical lows. Objective algorithms are used to track these features in CMIP5 model output. It is then established that the climatological locations and frequencies of these systems are reasonably well represented in the CMIP5 models. RCP8.5 end-of-twenty-first-century projections are compared with historical end-of-twentieth-century simulations. Future projections in tropical-low locations and frequencies diverge, but indicate an overall average decrease of 15% and in some cases a northward shift. The projected spatial change in the tropical-low frequency distribution is weakly positively correlated to the projected spatial change in the austral summer rainfall distribution. Meanwhile, future projections indicate a 13% increase in CAB frequency from October to December. This is associated with the gradual climatological CAB breakdown occurring half a month later on average in end-of-twenty-first-century RCP8.5 projections. A delay in the gradual seasonal decline of the CAB prevents rainfall to the south of the CAB’s mean position, most of which is shown to occur on CAB breakdown days, hence creating the austral spring drying signal and delayed wet-season onset. Intermodel variability in the magnitude of CAB frequency increase is able to explain intermodel variability in the projected drying.
Why Is the Mediterranean a Climate Change Hot Spot?
Authors: Tuel A. , Eltahir E. A. B. 
Published: May 2020

AbstractHigher precipitation is expected over most of the world’s continents under climate change, except for a few specific regions where models project robust declines. Among these, the Mediterranean stands out as a result of the magnitude and significance of its winter precipitation decline. Locally, up to 40% of winter precipitation could be lost, setting strong limits on water resources that will constrain the ability of the region to develop and grow food, affecting millions of already water-stressed people and threatening the stability of this tense and complex area. To this day, however, a theory explaining the special nature of this region as a climate change hot spot is still lacking. Regional circulation changes, dominated by the development of a strong anomalous ridge, are thought to drive the winter precipitation decline, but their origins and potential contributions to regional hydroclimate change remain elusive. Here, we show how wintertime Mediterranean circulation trends can be seen as the combined response to two independent forcings: robust changes in large-scale, upper-tropospheric flow and the reduction in the regional land–sea temperature gradient that is characteristic of this region. In addition, we discuss how the circulation change can account for the magnitude and spatial structure of the drying. Our findings pave the way for better understanding and improved modeling of the future Mediterranean hydroclimate.
Measured and Modeled Historical Precipitation Trends for Svalbard
Authors: Førland Eirik J. , Isaksen Ketil , Lutz Julia , Hanssen-Bauer Inger , Schuler Thomas Vikhamar , Dobler Andreas , Gjelten Herdis M. , Vikhamar-Schuler Dagrun 
Published: May 2020

AbstractPrecipitation plays an important role in the Arctic hydrological cycle, affecting different areas like the surface energy budget and the mass balance of glaciers. Thus, accurate measurements of precipitation are crucial for physical process studies, but gauge measurements in the Arctic are sparse and subject to relocations and several gauge issues. From Svalbard, we analyze precipitation trends at six weather stations for the last 50–100 years by combining different observation series and adjusting for inhomogeneities. For the past 50 years, the measured annual precipitation has increased by 30%–45%. However, precipitation measurements in the cold and windy climate are strongly influenced by gauge undercatch. Correcting for undercatch reduces the trend values by 10% points, since the fraction of solid precipitation has decreased and undercatch is larger for solid precipitation. Thus, precipitation corrected for undercatch should be used to study “true” precipitation trends in the Arctic. Precipitation over Svalbard has been modeled by downscaling reanalysis data to a spatial resolution of 1 km. In general, the modeled annual precipitation is higher (13%–175%) than the measured values and mainly higher than the precipitation corrected for undercatch. Although the model resolves orographic effects on a regional scale, the downscaling is not able to reproduce local orographic enhancement for onshore winds, nor local effects of rain shadow. The downscaled dataset explains approximately 60% of the interannual precipitation variability. The model-based trends during 1979–2018 are positive, but weaker (~4% decade−1) than the observed (~8% decade−1) trends.
Head and Neck Tumor Resection and Free Flap Reconstruction in Low-Volume Center
Authors: Brennan Malia , Wong Shelley , Faringer Paul D. , Lim Jae H. 
Published: May 2020

Objective: To determine the surgical outcomes of free tissue transfer surgery following head and neck tumor extirpation in a low-volume medical center. Methods: Retrospective chart review of patients who underwent free tissue transfer surgery for head and neck cancer at Moanalua Medical Center from 2015 to 2018. Main Outcome of Measure: Free flap failure rate and free flap-related complications. Results: From 2015 to 2018, there were 27 free tissue transfer surgery (mean 6.75 flap surgery/year). There were 2 events of partial flap necrosis, and no cases of total flap loss. One patient required leech therapy for venous congestion. One patient required additional free flap surgery. Two patients developed orocutaneous fistula that resolved with local wound care. One patient developed malocclusion following mandible reconstruction using fibular free flap. Overall free flap success rate was 96%. Conclusion: This study supports the ability of small-volume centers to produce positive outcomes with few complications in head and neck cancer free flap reconstructive surgery. While the data are limited to a single surgical team in one care center, it provides additional support for the idea that there are factors beyond the surgical volume that determine outcome.