bluuebunny/crossref_metadata_2025_split huggingface dataset:
Desmoplastic Infantile Ganglioglioma/Astrocytoma (DIG/DIA) Are Distinct Entities with Frequent BRAFV600 Mutations
Authors: Wang Anthony C. , Jones David T.W. , Abecassis Isaac Joshua , Cole Bonnie L. , Leary Sarah E.S. , Lockwood Christina M. , Chavez Lukas , Capper David , Korshunov Andrey , Fallah Aria , Wang Shelly , Ene Chibawanye , Olson James M. , Geyer J. Russell , Holland Eric C. , Lee Amy , Ellenbogen Richard G. , Ojemann Jeffrey G. 
Published: July 2018

Abstract
Desmoplastic infantile ganglioglioma (DIG) and desmoplastic infantile astrocytoma (DIA) are extremely rare tumors that typically arise in infancy; however, these entities have not been well characterized in terms of genetic alterations or clinical outcomes. Here, through a multi-institutional collaboration, the largest cohort of DIG/DIA to date is examined using advanced laboratory and data processing techniques. Targeted DNA exome sequencing and DNA methylation profiling were performed on tumor specimens obtained from different patients (n = 8) diagnosed histologically as DIG/DIGA. Two of these cases clustered with other tumor entities, and were excluded from analysis. The remaining 16 cases were confirmed to be DIG/DIA by histology and by DNA methylation profiling. Somatic BRAF gene mutations were discovered in 7 instances (43.8%); 4 were BRAFV600E mutations, and 3 were BRAFV600D mutations. Three instances of malignant transformation were found, and sequencing of the recurrence demonstrated a new TP53 mutation in one case, new ATRX deletion in one case, and in the third case, the original tumor harbored an EML4–ALK fusion, also present at recurrence. DIG/DIA are distinct pathologic entities that frequently harbor BRAFV600 mutations. Complete surgical resection is the ideal treatment, and overall prognosis is excellent. While, the small sample size and incomplete surgical records limit a definitive conclusion about the risk of tumor recurrence, the risk appears quite low. In rare cases with wild-type BRAF, malignant progression can be observed, frequently with the acquisition of other genetic alterations.
Implications: DIG/DIA are a distinct molecular entity, with a subset frequently harboring either BRAFV600E or BRAFV600D mutations. Mol Cancer Res; 16(10); 1491–8. ©2018 AACR.
Atrophied Thymus, a Tumor Reservoir for Harboring Melanoma Cells
Authors: Sizova Olga , Kuriatnikov Denis , Liu Ying , Su Dong-Ming 
Published: July 2018

Abstract
Tumor metastatic relapse is the primary cause for cancer-associated mortality. Metastatic relapse is believed to arise from quantities of tumor cells that are below detectable thresholds, which are able to resist radio/chemotherapy by obtaining a dormant state and hiding in certain organs, i.e., tumor reservoirs. The thymus, a central T-cell immune organ, has been suggested to be a premetastatic tumor reservoir for B-lymphoma cells. However, it remains unknown whether the thymus is able to harbor nonlymphoid solid tumor cells, and whether chemotherapy can thoroughly eliminate cancer cells in the thymus. If chemotherapy is not able to eliminate these cells in the thymus, then what processes allow for this? Melanoma cell–inoculated and genotoxic doxorubicin-treated mouse model systems were used to determine that the thymus, particularly the atrophied thymus, was able to harbor blood stream–circulating melanoma cells. In addition, a chemotherapy-induced DNA-damage response triggered p53 activation in nonmalignant thymic cells, which in turn resulted in thymocyte death and thymic epithelial cell senescence to develop an inflammatory thymic microenvironment. This inflammatory condition induced thymic-harbored minimal tumor cells to acquire a chemoresistant state.
Implications: Here, the thymus serves as a premetastatic reservoir for nonlymphoid solid tumor cells during chemotherapy, which could be a novel target of minimal residual disease in antitumor therapy, thus preventing tumor metastatic relapse. Mol Cancer Res; 16(11); 1652–64. ©2018 AACR.
Is Perfusion MRI without Deconvolution Reliable for Mismatch Detection in Acute Stroke? Validation with <sup>15</sup>O-Positron Emission Tomography
Authors: Reimer Johanna , Montag Cornelia , Schuster Alexander , Moeller-Hartmann Walter , Sobesky Jan , Heiss Wolf-Dieter , Zaro-Weber Olivier 
Published: July 2018

<b><i>Background:</i></b> In acute stroke, the magnetic resonance (MR) imaging-based mismatch concept is used to select patients with tissue at risk of infarction for reperfusion therapies. There is however a controversy if non-deconvolved or deconvolved perfusion weighted (PW) parameter maps perform better in tissue at risk prediction and which parameters and thresholds should be used to guide treatment decisions. <b><i>Methods:</i></b> In a group of 22 acute stroke patients with consecutive MR and quantitative positron emission tomography (PET) imaging, non-deconvolved parameters were validated with the gold standard for penumbral-flow (PF) detection <sup>15</sup>O-water PET. Performance of PW parameters was assessed by a receiver operating characteristic curve analysis to identify the accuracy of each PWI map to detect the ­upper PF threshold as defined by PET cerebral blood flow &#x3c;20 mL/100 g/min. <b><i>Results:</i></b> Among normalized non-deconvolved parameters, PW-first moment without delay correction (FM without DC) &#x3e; 3.6 s (area under the curve [AUC] = 0.89, interquartile range [IQR] 0.85–0.94), PW-maximum of the concentration curve (Cmax) &#x3c; 0.66 (AUC = 0.92, IQR 0.84–0.96) and PW-time to peak (TTP) &#x3e; 4.0 s (AUC = 0.92, IQR 0.87–0.94) perform significantly better than other non-deconvolved parameters to detect the PF threshold as defined by PET. <b><i>Conclusions:</i></b> Non-deconvolved parameters FM without DC, Cmax and TTP are an observer-independent alternative to established deconvolved parameters (e.g., Tmax) to guide treatment decisions in acute stroke.
High-Risk Types of Human Papilloma Virus DNA Testing in Women with False Negative Cytology
Authors: Edblad-Svensson Ann , Silfverdal Lena , Collberg Pia , Tunón Katarina 
Published: July 2018

<b><i>Objective:</i></b> To determine whether high-risk types of human papilloma virus (hrHPV) DNA testing is reliable for selection patients in need of further investigation with colposcopy in women with increased risk of high-grade cervical lesions as a result of false negative cytology. The secondary objective was to compare the sensitivity of hrHPV testing on self-collected versus physician-collected samples for the detection of histological high-grade cervical intraepithelial neoplasia (CIN2+). <b><i>Methods:</i></b> Sixty-three patients identified with a missed abnormality following the re-evaluation of benign cervical cytology were included. A patient-collected and a physician-collected sample for HPV, colposcopy and cervical specimen collection for histology and cytology were performed. <b><i>Results:</i></b><i></i> The sensitivity of hrHPV testing of physician-collected samples for CIN2+ was 100% (95% CI 82.7–100), and the negative predictive value (NPV) was 100% (95% CI 93.3–100). The sensitivity of the self-sampling device to identify CIN2+ was 84.6% (95% CI 59.1–96.7), and the NPV was 94.4% (95% CI 83.4–98.8). The differences in the sensitivity and NPV between the 2 methods were non-significant. The agreement between the 2 methods regarding the HPV results was good, with a kappa value of 0.74 (95% CI 0.57–0.91). <b><i>Conclusion:</i></b> The current findings indicate that physician-collected samples for hrHPV DNA testing may be used as triage for the colposcopy of women with false negative cytology.
Home-Based Care Evolution in Chronic Respiratory Failure between 2001 and 2015 (Antadir Federation Observatory)
Authors: Melloni Boris , Mounier Line , Laaban Jean-Pierre , Chambellan Arnaud , Foret Didier , Muir Jean-François 
Published: July 2018

<b><i>Background:</i></b> The aetiologies of chronic respiratory failure (CRF) are moving in many western countries. Obesity-Hypoventilation syndrome (OHS) has become one of the most common indications of non-invasive ventilation (NIV) with Chronic Obstructive Pulmonary Diseases (COPD). Long-Term Oxygen Therapy (LTOT) technology is the treatment plan for CRF patients in the new era. <b><i>Objectives:</i></b> This study aimed to assess home-based care evolution in CRF patients on LTOT (LTOT) and/or NIV from the ANTADIR observatory. <b><i>Methods:</i></b> A computerized database from 14 regional facilities was analysed (30% of French home-treated patients). Patient age, sex, aetiology, home respiratory devices were recorded between 2001 and 2015. <b><i>Results:</i></b> By the end of 2015, 12,147 CRF patients received LTOT (40%), NIV (24%), LTOT + NIV (23%), continuous positive airway pressure (CPAP; 11%) or LTOT + CPAP (3%). Between 2001 and 2015, we observed a decrease of LTOT (63–40%) in the benefit of NVI ± LTOT (25–47%). Regarding the aetiology, we note a slight decrease in obstructive disease and a significant increase in restrictive disease, mainly due to OHS. The 10-year survival was better on NIV ± LTOT than on LTOT, for overall patients and for both obstructive and restrictive patients. The 10-year survival was better on NIV ± LTOT than on LTOT (35 vs. 10%, <i>p</i> &#x3c; 0.05). In COPD patients on LTOT, a switch from conventional to new home devices was observed. Stationary LTOT systems were less prescribed, while portable/transportable ­system, liquid oxygen and self-filling oxygen were increasingly prescribed. <b><i>Conclusion:</i></b> Our study confirmed changes in CRF aetiologies and home devices. OHS is now an important indication of NIV. Using new LTOT technologies changed home prescriptions in COPD patients.
Variable Vowel Metaphony in Asturian: An Acoustic Analysis
Authors: Barnes Sonia 
Published: July 2018

Abstract
Background/Aims: Vowel metaphony, a type of vowel harmony observed in Asturian, is characterized by the raising and/or centralization of stressed mid or low vowels in the presence of a high vowel in word-final position. Descriptions of Asturian metaphony have been based on data collected using exclusively auditory judgments. This study is the first to document the phenomenon acoustically. Methods: The data were collected using a word elicitation task and sociolinguistic interviews of 40 speakers from the 2 geographic areas in which metaphony has been observed. Qualitative and quantitative analyses of vocalic distributions were performed. Results: The results of the analyses show that: (1) while metaphony still occurs in Asturian, its implementation is highly variable; (2) metaphonized variants remain distinct from other vowels; and (3) the traditional distinction between 2 areas of metaphony cannot be maintained. Conclusion: This study provides the first acoustic characterization of vowel metaphony in Asturian, offering empirical evidence on which to build theoretical approaches to vowel metaphony.
Endothelial Microparticles and Systemic Complement Activation in Patients With Chronic Kidney Disease
Authors: Jalal Diana , Renner Brandon , Laskowski Jennifer , Stites Erik , Cooper James , Valente Karissa , You Zhiying , Perrenoud Loni , Le Quintrec Moglie , Muhamed Ismaeel , Christians Uwe , Klawitter Jelena , Lindorfer Margaret A. , Taylor Ronald P. , Holers V. Michael , Thurman Joshua M. 
Published: July 2018

Background

Endothelial microparticles are associated with chronic kidney disease (
CKD
) and complement activation. We hypothesized that the complement pathway is activated in patients
with CKD
via endothelial microparticles and that complement activation correlates with endothelial dysfunction in
CKD
.

Methods and Results

We analyzed complement data of 30 healthy subjects, 30 patients with stage
III
/
IV CKD
, and 30 renal transplant recipients with stage
III
/
IV CKD
, evaluating the potential correlation of complement fragments with brachial artery flow–mediated dilation, Chronic Kidney Disease Epidemiology Collaboration glomerular filtration rate, and urinary albumin/creatinine ratio. Endothelial microparticles were characterized via proteomic analysis and compared between study groups. Complement fragment Ba was significantly increased in
CKD
and post–kidney transplant
CKD
. Plasma Ba levels correlated significantly with lower brachial artery flow–mediated dilation, lower Chronic Kidney Disease Epidemiology Collaboration glomerular filtration rate, and higher urinary albumin/creatinine ratio. Factor D levels were significantly higher in the plasma microparticles of patients with CKD versus healthy controls. Plasma microparticles isolated from patients with CKD and containing factor D activated the alternative pathway in vitro.

Conclusion

The alternative complement pathway is activated in
CKD
and correlates with endothelial dysfunction and markers of
CKD
. Future studies are needed to evaluate whether endothelial microparticles with increased factor D play a pathologic role in
CKD
‐associated vascular disease.

Clinical Trial Registration

URL
:
http://www.clinicaltrials.gov
. Unique identifier:
NCT
02230202.
Coronary Plaque Characteristics in Patients With Diabetes Mellitus Who Presented With Acute Coronary Syndromes
Authors: Sugiyama Tomoyo , Yamamoto Erika , Bryniarski Krzysztof , Xing Lei , Fracassi Francesco , Lee Hang , Jang Ik‐Kyung 
Published: July 2018

Background

Diabetes mellitus (
DM
) is a major risk factor for cardiovascular events. We aimed to investigate the coronary plaque phenotype of diabetic patients who presented with acute coronary syndromes by optical coherence tomography.

Methods and Results

A total of 322 patients with acute coronary syndromes who underwent preintervention optical coherence tomography imaging of the culprit lesion were included. Culprit plaque characteristics were compared between patients with
DM
(n=95) and those without
DM
(n=227). In the subgroup of 250 patients in whom sufficient length of nonculprit region in the culprit vessel was imaged by optical coherence tomography, the characteristics of nonculprit plaques were also evaluated. Patients with
DM
had a higher prevalence of lipid‐rich plaque (58.9% versus 44.9%,
P
=0.030) and macrophage accumulation (60.0% versus 44.9%,
P
=0.019) in the culprit lesion compared with patients without
DM
. The prevalence of plaque rupture (33.7% versus 30.4%,
P
=0.896) and plaque erosion (21.1% versus 22.0%,
P
=0.458) was similar. In the nonculprit lesions, the
DM
group had greater maximal lipid arc (248.9°±83.9° versus 179.9°±58.3°,
P
=0.006), thinner fibrous cap thickness (103.3±56.2 μm versus 140.7±70.0 μm,
P
=0.013), and a higher prevalence of thin‐cap fibroatheroma (17.2% versus 6.3%,
P
=0.031), compared with the non‐
DM
group.

Conclusions

Compared with patients without
DM
, those with
DM
had more vulnerable features in both culprit and nonculprit lesions, thus indicating a higher level of panvascular instability.

Clinical Trial Registration

URL
:
http://www.clinicaltrials.gov
. Unique identifier:
NCT
01110538.
Anaphora With Non-nominal Antecedents in Computational Linguistics: a Survey
Authors: Kolhatkar Varada , Roussel Adam , Dipper Stefanie , Zinsmeister Heike 
Published: July 2018

This article provides an extensive overview of the literature related to the phenomenon of non-nominal-antecedent anaphora (also known as abstract anaphora or discourse deixis), a type of anaphora in which an anaphor like “that” refers to an antecedent (marked in boldface) that is syntactically non-nominal, such as the first sentence in “It’s way too hot here. That’s why I’m moving to Alaska.” Annotating and automatically resolving these cases of anaphora is interesting in its own right because of the complexities involved in identifying non-nominal antecedents, which typically represent abstract objects such as events, facts, and propositions. There is also practical value in the resolution of non-nominal-antecedent anaphora, as this would help computational systems in machine translation, summarization, and question answering, as well as, conceivably, any other task dependent on some measure of text understanding. Most of the existing approaches to anaphora annotation and resolution focus on nominal-antecedent anaphora, classifying many of the cases where the antecedents are syntactically non-nominal as non-anaphoric. There has been some work done on this topic, but it remains scattered and difficult to collect and assess. With this article, we hope to bring together and synthesize work done in disparate contexts up to now in order to identify fundamental problems and draw conclusions from an overarching perspective. Having a good picture of the current state of the art in this field can help researchers direct their efforts to where they are most necessary. Because of the great variety of theoretical approaches that have been brought to bear on the problem, there is an equally diverse array of terminologies that are used to describe it, so we will provide an overview and discussion of these terminologies. We also describe the linguistic properties of non-nominal-antecedent anaphora, examine previous annotation efforts that have addressed this topic, and present the computational approaches that aim at resolving non-nominal-antecedent anaphora automatically. We close with a review of the remaining open questions in this area and some of our recommendations for future research.
Herps without borders: a new newt case and a review of transalpine alien introductions in western Europe
Authors: Dubey Sylvain , Lavanchy Guillaume , Thiébaud Jacques , Dufresnes Christophe 
Published: July 2018

Abstract
Biogeographic processes have led to different evolutionary taxa occurring in the northern and southern edges of the Alpine Mountains in Western Europe. The integrity of this diversity is being challenged by frequent human-mediated trans-alpine translocations, sometimes leading to biological invasions. Several alien terrestrial vertebrates of south Alpine origins (Italy, Swiss Ticino) are causing damages to native north Alpine fauna. In this paper, we used molecular tools to characterize the understudied case of the Mediterranean smooth newt (Lissotriton vulgaris meridionalis) expanding in the outskirts of Geneva since its introduction before 1975. Mitochondrial and nuclear DNA sequencing suggest that these exotic populations are a mixture between two diverged L. v. meridionalis lineages from central Italy, and traces of potential hybridization with the native L. v. vulgaris was detected. This situation echoes many other trans-alpine alien introductions. We review all comparable cases of southern to northern Alps introductions in vertebrates, including seven reptiles and four amphibians. The majority of south alpine alien lineages were presumably imported voluntarily by enthusiasts and appear to perform better in the disturbed habitats found in the anthropogenic landscapes of Western Europe compared to their native north Alpine counterparts. Most pose serious threats to related species of similar ecology, through direct competition, predation and introgressive hybridization. Difficulties to detect alien species on time lead to significant conservation costs. Better education together with more appropriate and reactive management plans will be necessary to limit the impact of future alien introductions.
Model Uncertainty in Cloud–Circulation Coupling, and Cloud-Radiative Response to Increasing CO2, Linked to Biases in Climatological Circulation
Authors: Lipat Bernard R. , Voigt Aiko , Tselioudis George , Polvani Lorenzo M. 
Published: July 2018

AbstractRecent analyses of global climate models suggest that uncertainty in the coupling between midlatitude clouds and the atmospheric circulation contributes to uncertainty in climate sensitivity. However, the reasons behind model differences in the cloud–circulation coupling have remained unclear. Here, we use a global climate model in an idealized aquaplanet setup to show that the Southern Hemisphere climatological circulation, which in many models is biased equatorward, contributes to the model differences in the cloud–circulation coupling. For the same poleward shift of the Hadley cell (HC) edge, models with narrower climatological HCs exhibit stronger midlatitude cloud-induced shortwave warming than models with wider climatological HCs. This cloud-induced radiative warming results predominantly from a subsidence warming that decreases cloud fraction and is stronger for narrower HCs because of a larger meridional gradient in the vertical velocity. A comparison of our aquaplanet results with comprehensive climate models suggests that about half of the model uncertainty in the midlatitude cloud–circulation coupling stems from this impact of the circulation on the large-scale temperature structure of the atmosphere, and thus could be removed by improving the climatological circulation in models. This illustrates how understanding of large-scale dynamics can help reduce uncertainty in clouds and their response to climate change.
Characteristics of Size Change of Tropical Cyclones Traversing the Philippines
Authors: Lin Shu-Jeng , Chou Kun-Hsuan 
Published: July 2018

Abstract
This study investigates the size changes of tropical cyclones (TCs) traversing the Philippines based on a 37-yr statistical analysis. TC size is defined by the radius of 30-kt (≈15.4 m s−1) wind speed (R30) from the best track data of the Japan Meteorological Agency. A total of 71 TCs passed the Philippines during 1979–2015. The numbers of size increase (SI; 36) and size decrease (SD; 34) cases are very similar; however, the last 15 years have seen more SI cases (17) than SD cases (11). SI and SD cases mostly occur along northerly and southerly paths, respectively, after TCs pass the Philippines. Before landfall, SI cases have small initial sizes and weak intensities, but SD cases have larger initial sizes and stronger intensities. After landfall, most SI cases are intensifying storms, and most SD cases are nonintensifying storms. Composite analyses of vertical wind shear, absolute angular momentum flux, relative humidity, and sea surface temperature between SI and SD cases are compared. All of these values are larger in SI cases than in SD cases. Furthermore, the interdecadal difference in the ratio of the numbers of SI to SD cases reveals an unusually high number of SI cases during 2001–15. The synoptic patterns between 1979–2000 and 2001–15 are analyzed. The high SI ratio in the latter period is related to strong southwesterly wind in the south of the South China Sea that raised relative humidity, warmed the sea surface, and increased import of angular momentum flux.
The Impact of Vertical Resolution in the Assimilation of GPS Radio Occultation Data
Authors: Ha Ji-Hyun , Kang Jeon-Ho , Choi Suk-Jin 
Published: July 2018

Abstract
The sensitivity of GPS radio occultation (GPSRO) bending angle assimilation to vertical resolution was studied within a global three-dimensional variational data assimilation (3DVAR) system. The sensitivity experiments were performed using different vertical resolutions of GPSRO data at 2 km, 1 km, 500 m, and 200 m. The assimilation of the higher vertical resolution GPSRO data showed better consistency in the analysis–forecast cycle in terms of the differences between GPSRO bending angle data and 6-h forecasts (O-F). This resulted in an improved analysis of the temperature, geopotential height, and wind in the mid-/upper-level troposphere by the hydrostatic response and the related model dynamics. It should be noted that the highest vertical resolution of the GPSRO data (200 m in this study) improved the forecasting skill level in terms of the root-mean-square error (against the European Centre for Medium-Range Weather Forecasts analysis) and the anomaly correlation of the geopotential height forecasting at 500 and 200 hPa in both the Northern and Southern Hemispheres. The benefits of assimilating higher vertical resolution GPSRO data were more pronounced in the upper-level troposphere, which was in agreement with previous studies using real GPSRO observations.