bluuebunny/crossref_metadata_2025_split huggingface dataset:
TCIApathfinder: An R Client for the Cancer Imaging Archive REST API
Authors: Russell Pamela , Fountain Kelly , Wolverton Dulcy , Ghosh Debashis 
Published: June 2018

Abstract
The Cancer Imaging Archive (TCIA) hosts publicly available deidentified medical images of cancer from over 25 body sites and over 30,000 patients. Over 400 published studies have utilized freely available TCIA images. Images and metadata are available for download through a web interface or a REST API. Here, we present TCIApathfinder, an R client for the TCIA REST API. TCIApathfinder wraps API access in user-friendly R functions that can be called interactively within an R session or easily incorporated into scripts. Functions are provided to explore the contents of the large database and to download image files. TCIApathfinder provides easy access to TCIA resources in the highly popular R programming environment. TCIApathfinder is freely available under the MIT license as a package on CRAN (https://cran.r-project.org/web/packages/TCIApathfinder/index.html) and from https://github.com/pamelarussell/TCIApathfinder.
Significance: These findings present a new tool, TCIApathfinder, the first client for The Cancer Imaging Archive (TCIA) for use in the highly popular R computing environment, that will dramatically lower the barrier of access to the valuable tools in TCIA. Cancer Res; 78(15); 4424–6. ©2018 AACR.
Using a Culturally Tailored Intervention to Increase Colorectal Cancer Knowledge and Screening among Hispanics in a Rural Community
Authors: Briant Katherine J. , Sanchez Janeth I. , Ibarra Genoveva , Escareño Monica , Gonzalez Nora E. , Jimenez Gonzalez Virginia , Marchello Nathan , Louie Stephanie , Thompson Beti 
Published: June 2018

Abstract
Background: Disparities in colorectal cancer incidence and mortality rates exist among racial/ethnic minorities, especially those living in rural areas. There is an urgent need to implement interventions to improve colorectal cancer screening behaviors among such groups, particularly those living in rural areas in the United States.
Methods: From a rural community of Hispanics, we recruited participants to attend home-based promotor(a)-led “home health parties” in which participants were taught about colorectal cancer screening; participants ages 50 and older were given a free fecal occult blood test (FOBT) kit to complete on their own. A pre- and posttest design was used to assess changes in colorectal cancer awareness, knowledge, and screening at baseline and at 1-month follow-up after the intervention.
Results: We observed a statistically significant increase in colorectal cancer screening awareness and knowledge among participants. Colorectal cancer screening rates with FOBT increased from 51.0% to 80%. There was also a statistically significant increase in social engagement, that is, the intent to speak to friends and relatives about colorectal cancer screening.
Conclusions: Findings indicate that culturally tailored colorectal cancer education facilitated by promotores in a rural environment, coupled with free stool-based test for colorectal cancer screening, is an effective way to increase colorectal cancer screening awareness, knowledge, and screening among Hispanics living in a rural area in Washington State.
Impact: Culturally tailored home health interventions have the potential to achieve Healthy People 2020 colorectal cancer screening goals in Hispanic rural communities. Cancer Epidemiol Biomarkers Prev; 27(11); 1283–8. ©2018 AACR.
Support for Pharmacist-Provided HPV Vaccination: National Surveys of U.S. Physicians and Parents
Authors: Shah Parth D. , Calo William A. , Marciniak Macary W. , Gilkey Melissa B. , Brewer Noel T. 
Published: June 2018

Abstract
Background: State laws about pharmacists providing human papillomavirus (HPV) vaccines vary considerably, limiting many pharmacists' ability to provide this important cancer prevention service. We characterized physician and parent support for pharmacist-provided HPV vaccination for adolescents who are past due for vaccination.
Methods: In 2014 to 2015, we conducted two national U.S. surveys of 776 primary care physicians (PCPs) and 1,504 parents of adolescents. Respondents indicated the extent to which they supported pharmacist-provided HPV vaccination for 13- to 17-year-olds who are past due. Respondents could endorse the provision unconditionally, or only if certain conditions were met, such as pharmacists receiving proper vaccination training. We used multivariable logistic regression to assess correlates of support.
Results: Most physicians (79%) and parents (81%) endorsed pharmacist-provided HPV vaccination if pharmacists had received proper vaccination training, reported vaccine doses to adolescents' PCP, and referred adolescents to PCPs for other health services. Family medicine physicians were more likely than pediatricians to support trained pharmacists providing HPV vaccination [OR = 1.62; 95% confidence interval (CI) 1.17–2.22]. Support was also higher among physicians who practiced in Western states (OR = 2.11; 95% CI, 1.30–3.40). Parents' odds of endorsing trained pharmacists provision of HPV vaccine increased with higher overall satisfaction with their pharmacy's services (OR = 1.10; 95% CI, 1.02–1.19), belief in pharmacists' competence in vaccination practices (OR = 1.42; 95% CI, 1.18–1.70), and overall vaccine confidence (OR = 1.30; 95% CI, 1.15–1.48).
Conclusions: To increase support for HPV vaccination services, pharmacists should raise awareness about their immunization training and standardize vaccination protocols that ensure coordination with primary care.
Impact: Stakeholders' feedback and buy-in is important to help guide expansion of HPV vaccination in pharmacies. Cancer Epidemiol Biomarkers Prev; 27(8); 970–8. ©2018 AACR.
Advanced Mucinous Colorectal Cancer: Epidemiology, Prognosis and Efficacy of Chemotherapeutic Treatment
Authors: Ott Claudia , Gerken Michael , Hirsch Daniela , Fest Petra , Fichtner-Feigl Stefan , Munker Stefan , Schnoy Elisabeth , Stroszczynski Christian , Vogelhuber Martin , Herr Wolfgang , Evert Matthias , Reng Michael , Schlitt Hans Jürgen , Klinkhammer-Schalke Monika , Teufel Andreas 
Published: June 2018

Background: The clinicopathological significance of the mucinous subtype of colorectal cancer (CRC) remains controversial. As of today, none of the current guidelines differentiate treatment with respect to mucinous or nonmucinous cancer. Due to the lack of substantiated data, best treatment remains unclear and the mucinous subtype of CRC is usually treated along the lines of recommendations for adenocarcinoma of the colon. Methods: We investigated an East-Bavarian cohort of 8,758 patients with CRC. These included 613 (7.0%) patients with a mucinous subtype, who were analyzed for assessing their characteristics in clinical course and for evaluating the efficacy of common chemotherapy protocols. Results and Conclusion: Mucinous CRC was predominantly located in the right hemicolon; it was diagnosed at more advanced stages and occurred with preponderance in women. A higher rate of G3/4 grading was observed at diagnosis (all p < 0.001). An association of mucinous CRC with younger age at initial diagnosis, previously reported by other groups, could not be confirmed. Patients with mucinous stage IV colon cancer demonstrated poorer survival (p = 0.006). In contrast, no differences in survival were observed for specific stages I–III colon cancer. Stage-dependent analysis of rectal cancer stages I–IV also showed no differences in survival. However, univariable overall analysis resulted in significant poorer survival of mucinous compared to nonmucinous rectal cancer (p = 0.029). Also, combined analysis of all patients with mucinous CRC revealed poorer overall survival (OS) of these patients compared to nonmucinous CRC patients (median 48.4 vs. 60.2 months, p = 0.049) but not in multivariable analysis (p = 0.089). Chemotherapeutic treatment showed comparable efficacy regarding OS for mucinous and nonmucinous cancers in both an adjuvant and palliative setting for colon cancer patients (p values comparing mucinous and nonmucinous cancers < 0.001–0.005).
Successful Feasibility Human Trial of a New Self-Expandable Percutaneous Pulmonary Valve (Pulsta Valve) Implantation Using Knitted Nitinol Wire Backbone and Trileaflet α-Gal–Free Porcine Pericardial Valve in the Native Right Ventricular Outflow Tract
Authors: Kim Gi Beom , Song Mi Kyoung , Bae Eun Jung , Park Eun-Ah , Lee Whal , Lim Hong-Gook , Kim Yong Jin 
Published: June 2018

Background—
Self-expandable percutaneous pulmonary valve implantation (PPVI) for native right ventricular outflow tract lesions is still in the clinical trial phase. The aim of this study is to present the result of feasibility study of a novel self-expandable knitted nitinol wire stent mounted with a treated trileaflet α-Gal–free porcine pericardial valve for PPVI.

Methods and Results—

A feasibility study using Pulsta valve (TaeWoong Medical Co, Gyeonggi-do, South Korea) was designed for patients with severe pulmonary regurgitation in the native right ventricular outflow tract, and 6-month follow-up outcomes were reviewed. Ten tetralogy of Fallot patients were enrolled. Before PPVI, severe pulmonary regurgitation (mean pulmonary regurgitation fraction, 45.5%±7.2%; range, 34.9%–56%) and enlarged right ventricular volume (mean indexed right ventricular end-diastolic volume, 176.7±14.3 mL/m
2
; range, 158.9–205.9 mL/m
2
) were present. The median age at PPVI was 21.7±6.5 years (range, 13–36 years). Five patients were successfully implanted with 28 mm and the other 5 with 26 mm valves loaded on the 18F delivery cable. No significant periprocedural complications were noted in any patient. At the 6-month follow-up, indexed right ventricular end-diastolic volume was dramatically decreased to 126.3±20.3 mL/m
2
(range, 99–164.2 mL/m
2
), and the mean value of peak instantaneous pressure gradient between the right ventricle and the pulmonary artery decreased from 6.8±3.5 mm Hg (range, 2–12 mm Hg) before PPVI to 5.7±6.7 mm Hg (range, 2–12 mm Hg) without significant pulmonary regurgitation. There was no adverse event associated with the valve.

Conclusions—
A feasibility study of the Pulsta valve for native right ventricular outflow tract lesions was completed successfully with planned Pulsta valve implantation and demonstrated good short-term effectiveness without serious adverse events.

Clinical Trial Registration—

URL:
https://www.clinicaltrials.gov
. Unique identifier: NCT02555319.
Histone Variant H2A.Z Is Required for the Maintenance of Smooth Muscle Cell Identity as Revealed by Single-Cell Transcriptomics
Authors: Yao Fang , Yu Peng , Li Yue , Yuan Xinli , Li Zheng , Zhang Tao , Liu Fei , Wang Yingbao , Wang Yin , Li Dandan , Ma Baihui , Shu Chang , Kong Wei , Zhou Bingying , Wang Li 
Published: June 2018

Background:
Histone variants endow chromatin with specific structures, and play essential roles in development and diseases. However, little is known about their roles in controlling cell identity in vascular diseases.

Methods:
Given the cell heterogeneity in atherosclerotic lesions, we applied single-cell RNA-Sequencing to analyze diseased human arteries, and identified histone variant H2A.Z as a key histone signature to maintain vascular smooth muscle cell (VSMC) identity.

Results:
We show that H2A.Z occupies genomic regions near VSMC marker genes, and its occupancy is decreased in VSMCs undergoing dedifferentiation. Mechanistically, H2A.Z occupancy preferentially promotes nucleosome turnover, and facilitates the recruitment of SMAD3 and MED1, thereby activating VSMC marker gene expression. In addition, H2A.Z expression is dramatically reduced at both mRNA and protein levels in diseased human vascular tissues compared to those in normal arteries. Notably, in vivo overexpression of H2A.Z rescues injury-induced loss of VSMC identity and neointima formation.

Conclusions:
Together, our data introduce dynamic occupancy of a histone variant as a novel regulatory basis contributing to cell fate decisions, and imply H2A.Z as a potential intervention node for vascular diseases.
Use of Biomarkers to Predict Specific Causes of Death in Patients With Atrial Fibrillation
Authors: Sharma Abhinav , Hijazi Ziad , Andersson Ulrika , Al-Khatib Sana M. , Lopes Renato D. , Alexander John H. , Held Claes , Hylek Elaine M. , Leonardi Sergio , Hanna Michael , Ezekowitz Justin A. , Siegbahn Agneta , Granger Christopher B. , Wallentin Lars 
Published: June 2018

Background:
Atrial fibrillation is associated with an increased risk of death. High-sensitivity troponin T, growth differentiation factor-15, NT-proBNP (N-terminal pro-B-type natriuretic peptide), and interleukin-6 levels are predictive of cardiovascular events and total cardiovascular death in anticoagulated patients with atrial fibrillation. The prognostic utility of these biomarkers for cause-specific death is unknown.

Methods:
The ARISTOTLE trial (Apixaban for the Prevention of Stroke in Subjects With Atrial Fibrillation) randomized 18 201 patients with atrial fibrillation to apixaban or warfarin. Biomarkers were measured at randomization in 14 798 patients (1.9 years median follow-up). Cox models were used to identify clinical variables and biomarkers independently associated with each specific cause of death.

Results:

In total, 1272 patients died: 652 (51%) cardiovascular, 32 (3%) bleeding, and 588 (46%) noncardiovascular/nonbleeding deaths. Among cardiovascular deaths, 255 (39%) were sudden cardiac deaths, 168 (26%) heart failure deaths, and 106 (16%) stroke/systemic embolism deaths. Biomarkers were the strongest predictors of cause-specific death: a doubling of troponin T was most strongly associated with sudden death (hazard ratio [HR], 1.48;
P
<0.001), NT-proBNP with heart failure death (HR, 1.62;
P
<0.001), and growth differentiation factor-15 with bleeding death (HR, 1.72;
P
=0.028). Prior stroke/systemic embolism (HR, 2.58;
P
>0.001) followed by troponin T (HR, 1.45;
P
<0.0029) were the most predictive for stroke/ systemic embolism death. Adding all biomarkers to clinical variables improved discrimination for each cause-specific death.

Conclusions:
Biomarkers were some of the strongest predictors of cause-specific death and may improve the ability to discriminate among patients’ risks for different causes of death. These data suggest a potential role of biomarkers for the identification of patients at risk for different causes of death in patients anticoagulated for atrial fibrillation.

Clinical Trial Registration:

URL:
https://www.clinicaltrials.gov
. Unique identifier: NCT00412984.
Spatial ecology of a small arboreal ambush predator, Trimeresurus macrops Kramer, 1977, in Northeast Thailand
Authors: Strine Colin , Silva Inês , Barnes Curt H. , Marshall Benjamin M. , Artchawakom Taksin , Hill Jacques , Suwanwaree Pongthep 
Published: June 2018

Abstract
The Big-Eyed Green Pit Viper (Trimeresurus macrops; Kramer, 1977) is a venomous snake species endemic to Southeast Asia. Although we have some knowledge of the systematics and toxicology of T. macrops, little is known about the spatial ecology of this species. From May 2013 to February 2014, we used radio-telemetry to determine home-range sizes of 13 adult female T. macrops inhabiting the Sakaerat Biosphere Reserve in Northeast Thailand. We found that individual home ranges for T. macrops averaged 0.175 ha, with activity areas ranging from 0.112-0.303 ha and core areas ranging from 0.023-0.052 ha. There was little overlap between conspecific tracked females, especially for the most used areas of their home ranges. We find that T. macrops ambushes more in higher humidity and expresses very little diurnal activity. They use the groundstory for ambushing, then retreat over small distances to higher refuge during the day. Future studies should focus on prey abundance, habitat selection, and survival rates.
Use of pitfall traps for sampling marine benthic arthropods on soft substrate
Authors: Dadaliaris M. , Grantounis P. , Evagelopoulos A. , Katsanevakis S. 
Published: June 2018

AbstractEcological monitoring is a prerequisite for ecosystem-based management and conservation. There is a need for developing an efficient and non-destructive method for monitoring marine benthic arthropods on soft substrate, as the currently applied methods are often inadequate. Pitfall trapping has been used extensively to sample terrestrial arthropods, but has not been seriously considered yet in the marine environment. In this study, the effectiveness of pitfall traps for monitoring marine benthic arthropods was assessed through a case study in the shallow sublittoral zone of Kalloni Gulf, Lesvos Island, Greece. Two different trap types were installed in August 2016 at five depths, during two 12 h periods (day and night). Pitfall traps performed well, collecting a large number of individuals. The hermit crabDiogenes pugilatordominated the catches. The catch of this species significantly differed by trap type, while the interaction between depth and period was also found significant. Further research is needed to evaluate the efficiency of different types of pitfall traps and field protocols in the marine environment.
Redescription of a Philippine endemic freshwater calanoid copepod, Pseudodiaptomus brehmi Kiefer, 1938 (Copepoda, Calanoida, Pseudodiaptomidae)
Authors: Guinto S. K. P. , Walter T. C. , Papa R. D. S. 
Published: June 2018

Abstract
The genus Pseudodiaptomus is represented by 19 species in Philippine coastal waters. Of all these species found in the Philippines, P. brehmi Kiefer, 1938 is the only known truly freshwater pseudodiaptomid endemic to this country, which was originally described from Lake Naujan, Mindoro Island. After numerous attempts to find it in its type locality, we concluded that the former is no longer extant in this lake and has now been displaced by the invasive Neotropical calanoid Arctodiaptomus dorsalis (Marsh, 1907). Sampling in Lake Taal, on the nearby island of Luzon, resulted in the surprise discovery of P. brehmi populations coexisting with A. dorsalis. This rediscovery of P. brehmi in Lake Taal and its absence from its type locality, necessitate this report as well as the species’ morphological redescription.
The presence of Macromedaeus distinguendus (De Haan, 1835) (Brachyura, Xanthidae) in the shallow hydrothermal vent system off northeastern Taiwan
Authors: Tseng Li-Chun , Limviriyakul Parinya , Ho Ping-Ho , Hwang Jiang-Shiou 
Published: June 2018

Abstract
The present study investigated the population of the xanthid brachyuran crab, Macromedaeus distinguendus (De Haan, 1835), at a toxic hydrogen sulfide, shallow hydrothermal vent area at Turtle Island, off northeastern Taiwan. This is the first record of this species from this extreme environment, and M. distinguendus is only the second brachyuran discovered in this area. The wet weight of male and female M. distinguendus varied from 0.11 to 1.22 g (mean ± standard deviation: 0.56 ± 0.39 g) and 0.06 to 0.62 g (0.37 ± 0.15 g), respectively. The wet weight: carapace width ratio was significantly correlated in both sexes. The local distribution patterns of M. distinguendus were different from those of the obligate hydrothermal crab Xenograpsus testudinatus N. K. Ng, J.-F. Huang & Ho, 2000 (Xenograpsidae) in this area. An analysis of resource use and habitat partitioning revealed that the two crab species were able to co-exist within the study area.
Ghost crab burrows simulation shows differential across-shore persistence
Authors: Campagnoli Mariana L. , Pombo Maíra , Turra Alexander 
Published: June 2018

Abstract
Ghost-crab abundance is often used as an indicator of sandy beach environmental quality. Most studies use an indirect approach, assuming a direct relationship between the number of burrows and individuals. We here hypothesized that burrows could remain open for different periods of time according to the beach strata. We performed a field manipulation to simulate burrows, with persistence of each one individually assessed over a month. Results succeeded in demonstrating a significant differential persistence of burrows among beach compartments (backshore, frontal dune, and coastal vegetation, i.e., in a landward oriented sequence), which can affect abundance estimates and are thus prone to overestimating larger size classes, which inhabit the landward limit of the species’ range of occurrence. We recommend that this information is taken into consideration in population studies, and encourage the development of similar studies over broader spatial and temporal scales.
Does colour matter? Genetic differentiation of colour morphs of the Asian golden web spider Nephila antipodiana (Araneae: Nephilidae)
Authors: Low Van Lun , Norma-Rashid Yusoff , Ubaidillah Rosichon , Yusoff Amri , Prakash Batah Kunalan , Tan Tiong Kai , Chen Chee Dhang , Sofian-Azirun Mohd 
Published: June 2018

Abstract
Here we present the first attempt to test for genetic differentiation among four distinct colour morphs of the Asian golden web spider Nephila antipodiana Walckenaer. Fragments of the 18S rRNA (18S) and cytochrome c oxidase subunit I (COI) genes were sequenced in eight populations of N. antipodiana belonging to four distinct colour morphs: yellow, yellowish green, and two newly discovered morphs, reddish yellow and white-spotted. The nuclear sequences amplified from females of the four colour morphs were identical. The mitochondrial COI sequences, on the other hand, revealed slightly higher variation by recovering three haplotypes belonging to two different clades. Clade I comprises yellow, yellowish green and reddish yellow morphs from the mainland of Southeast Asia and Java, whereas clade II is restricted to white-spotted morph originating from Borneo. The low genetic divergence between both clades, despite being distinctive, undoubtedly provides new insight into the genetic diversity of this polymorphic species.
100 Years of Research on Mesoscale Convective Systems
Authors: Houze Robert A. 
Published: June 2018

Abstract
When cumulonimbus clouds aggregate, developing into a single entity with precipitation covering a horizontal scale of hundreds of kilometers, they are called mesoscale convective systems (MCSs). They account for much of Earth’s precipitation, generate severe weather events and flooding, produce prodigious cirriform anvil clouds, and affect the evolution of the larger-scale circulation. Understanding the inner workings of MCSs has resulted from developments in observational technology and modeling. Time–space conversion of ordinary surface and upper-air observations provided early insight into MCSs, but deeper understanding has followed field campaigns using increasingly sophisticated radars, better aircraft instrumentation, and an ever-widening range of satellite instruments, especially satellite-borne radars. High-resolution modeling and theoretical insights have shown that aggregated cumulonimbus clouds induce a mesoscale circulation consisting of air overturning on a scale larger than the scale of individual convective up- and downdrafts. These layers can be kilometers deep and decoupled from the boundary layer in elevated MCSs. Cooling in the lower troposphere and heating aloft characterize the stratiform regions of MCSs. As a result, long-lived MCSs with large stratiform regions have a top-heavy heating profile that generates potential vorticity in midlevels, thus influencing the larger-scale circulation within which the MCSs occur. Global satellite data show MCSs varying in structure, depending on the prevailing large-scale circulation and topography. These patterns are likely to change with global warming. In addition, environmental pollution affects MCS structure and dynamics subtly. Feedbacks of MCSs therefore need to be included or parameterized in climate models.