bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electroweak corrections to the angular coefficients in finite-$$p_T$$ Z-boson production and dilepton decay
Authors: Frederix Rikkert , Vitos Timea 
Published: October 2020

AbstractWe present next-to-leading order (NLO) electroweak corrections to the dominant five angular coefficients parametrizing the Drell–Yan process in the Z-boson mass peak range for finite-$$p_T$$

p
T

vector boson production. The results are presented differentially in the vector boson transverse momentum. The Lam–Tung violating difference $$A_0-A_2$$

A
0

-

A
2

is examined alongside the coefficients. A single lepton transverse momentum cut is needed in the case of electroweak corrections to avoid a double singularity in the photon induced diagrams, and the dependence on the value of this cut is examined. We compare the electroweak corrections to the angular coefficients to the NLO QCD corrections, including the single lepton cut. The size of the single lepton cut is found to affect the two coefficients $$A_0$$

A
0

and $$A_2$$

A
2

to largest extent. The relative size of the electroweak corrections to the coefficients is moderate for all single lepton cut values, and by extrapolation to the inclusive results, is moderate also for the full dilepton phase space case. However, for the Lam–Tung violation, there is a significant contribution from the electroweak corrections for low $$p_T$$

p
T

of the lepton pair.
On the surjectivity of certain word maps on SU(2)
Authors: Khoi Vu The , Toan Ho Minh 
Published: October 2020

In this paper, we study the word map [Formula: see text] where [Formula: see text] is a word in the free group [Formula: see text] of rank 2. We give a necessary and sufficient condition for the surjectivity of the word map by using the trace polynomials. As applications of our method, we give example of word [Formula: see text] for which the word map is not surjective. For families of words belonging to [Formula: see text] of the form [Formula: see text] and [Formula: see text] we can tell whether the word map is surjective or not.
Seismic-scale geometries and sequence-stratigraphic architecture of Early Cretaceous syn-post rift carbonate systems, Presalt Section, Brazil
Authors: Minzoni M. , Cantelli A. , Thornton J. , Wignall B. 
Published: October 2020

Abstract
Regional and detailed seismic stratigraphic analyses of Early Cretaceous (Aptian) presalt carbonate sections from offshore Brazil reveal the complex stratigraphic architecture of late- and post-rift lacustrine carbonate systems. The lateral and vertical distribution of calibrated seismic facies within this framework highlights the evolution through time of the carbonate system and bathymetry of the host lacustrine basin. Despite the simple, largely abiotic and microbial components, lacustrine carbonate accumulations formed complex geometries that closely resemble those observed from marine systems, suggesting that a downward-tapering carbonate production profile must have occurred. The complexity of the stratigraphic architecture reflects lateral variations in subsidence patterns combined with the interference of the basement topography, palaeowind directions and basinal filling patterns. Well-imaged clinoforms several hundred metres high attest to both the existence of significant lake-bottom topography, locally in excess of 800 m, and the occurrence of deep water at time of deposition. Platform margin trajectory and vertical and lateral architecture of clinoform packages through time reveal distinct sequence boundaries that can be correlated in detail only locally, demonstrating the impact of syndepositional tectonics, and possibly recurrent isolation of smaller lakes during lowstands. Depositional models from this study fill a gap in current understanding of lacustrine carbonate systems and offer a template for exploration and appraisal of the presalt play.
Announcing biblatex-software
Authors: Di Cosmo Roberto 
Published: October 2020

Software, and software source code in particular, is widely used in modern research. It must be properly archived, referenced, described and cited in order to build a stable and long lasting corpus of scienti c knowledge. And yet, up to now there was no speci c support for citing software in the popular BibTeX format that we use for our bibliographies.
We got used to work around this lack of dedicated support by tweaking the @misc entry, citing the user manual, or an article related to a software artifact, or adding in the text or in a footnote urls pointing to a place where one could get the software: the project web page, or a code hosting platform.
These workaround were a manifestation of the fact that software artifacts themselves were not considered rst class citizen in the scholarly world.
With the recent raise of interest on reproducibility of research re- sults, from Artifact Evaluation Committees to the ACM Badges, we have started moving towards giving nally software the aca- demic dignity it deserves.
Holding on to Junk Bonds: Intron Retention in Cancer and Therapy
Authors: Monteuuis Geoffray , Schmitz Ulf , Petrova Veronika , Kearney Padraic S. , Rasko John E.J. 
Published: October 2020

Abstract
Intron retention (IR) in cancer was for a long time overlooked by the scientific community, as it was previously considered to be an artifact of a dysfunctional spliceosome. Technological advancements made in the last decade offer unique opportunities to explore the role of IR as a widespread phenomenon that contributes to the transcriptional diversity of many cancers. Numerous studies in cancer have shed light on dysregulation of cellular mechanisms that lead to aberrant and pathologic IR. IR is not merely a mechanism of gene regulation, but rather it can mediate cancer pathogenesis and therapeutic resistance in various human diseases. The burden of IR in cancer is governed by perturbations to mechanisms known to regulate this phenomenon and include epigenetic variation, mutations within the gene body, and splicing factor dysregulation. This review summarizes possible causes for aberrant IR and discusses the role of IR in therapy or as a consequence of disease treatment. As neoepitopes originating from retained introns can be presented on the cancer cell surface, the development of personalized cancer vaccines based on IR-derived neoepitopes should be considered. Ultimately, a deeper comprehension about the origins and consequences of aberrant IR may aid in the development of such personalized cancer vaccines.
The Effect of the Variability in Fecal Immunochemical Test Sample Collection Technique on Clinical Performance
Authors: Symonds Erin L. , Fraser Callum G. , Bastin Dawn , Berwald Grace , Young Graeme P. 
Published: October 2020

Abstract

Background:
Fecal immunochemical test (FIT) performance can be affected by post-collection variables. Collection technique might also affect fecal hemoglobin concentration (f-Hb). Variation in quantity of feces collected in samples returned in a colorectal cancer detection program, and the effects of under-sampling, were assessed.

Methods:
Collection devices obtained from patients undergoing FIT were assessed for the color (in five classes) of the feces in buffer, mass, and f-Hb. Associations between these were examined in an in vitro study on Hb-spiked feces. Variables possibly associated with under-sampling were investigated using multivariable logistic regression. The effect of low sample mass on clinical performance (false-negative results) was determined.

Results:
Of 6,898 samples collected by 3,449 individuals (46.9% male, median age: 65.3 years), the buffer was lightest in color in 362 (5.2%), and darkest in 420 (6.1%). Samples with the lightest color had a significantly lower f-Hb compared with all darker classes (P &lt; 0.001). Mass was recorded for 650 devices: The lightest colored samples had significantly lower mass (P &lt; 0.05). The correlation between mass and f-Hb was confirmed in vitro (r = 0.897, P &lt; 0.001). Low mass was not associated with age, sex, or technical factors (P &gt; 0.05). Under-sampling related to the lightest color was not associated with false-negative results for colorectal cancer and advanced adenoma, but was for all neoplasia and inflammatory bowel disease.

Conclusions:
Wide variation existed in the amount of feces collected. Under-sampling results in lower measured f-Hb and may increase false-negative results.

Impact:
Color of sample buffer could be used to identify inadequate sampling.
Three Distinct Stroma Types in Human Pancreatic Cancer Identified by Image Analysis of Fibroblast Subpopulations and Collagen
Authors: Ogawa Yurina , Masugi Yohei , Abe Tokiya , Yamazaki Ken , Ueno Akihisa , Fujii-Nishimura Yoko , Hori Shutaro , Yagi Hiroshi , Abe Yuta , Kitago Minoru , Sakamoto Michiie 
Published: October 2020

Abstract

Purpose:
Cancer-associated fibroblasts have emerged to be highly heterogenous and can play multifaceted roles in dictating pancreatic ductal adenocarcinoma (PDAC) progression, immunosuppression, and therapeutic response, highlighting the need for a deeper understanding of stromal heterogeneity between patients and even within a single tumor. We hypothesized that image analysis of fibroblast subpopulations and collagen in PDAC tissues might guide stroma-based patient stratification to predict clinical outcomes and tumor characteristics.

Experimental Design:
A novel multiplex IHC-based image analysis system was established to digitally differentiate fibroblast subpopulations. Using whole-tissue slides from 215 treatment-naïve PDACs, we performed concurrent quantification of principal fibroblast subpopulations and collagen and defined three stroma types: collagen-rich stroma, fibroblast activation protein α (FAP)-dominant fibroblast-rich stroma, and α smooth muscle actin (ACTA2)-dominant fibroblast-rich stroma. These stroma types were assessed for the associations with cancer-specific survival by multivariable Cox regression analyses and with clinicopathologic factors, including CD8+ cell density.

Results:
FAP-dominant fibroblasts and ACTA2-dominant fibroblasts represented the principal distinct fibroblast subpopulations in tumor stroma. Stroma types were associated with patient survival, SMAD4 status, and transcriptome signatures. Compared with FAP-dominant fibroblast-rich stroma, collagen-rich stroma correlated with prolonged survival [HR, 0.57; 95% confidence interval (CI), 0.33–0.99], while ACTA2-dominant fibroblast-rich stroma exhibited poorer prognosis (HR, 1.65; 95% CI, 1.06–2.58). FAP-dominant fibroblast-rich stroma was additionally characterized by restricted CD8+ cell infiltrates and intense neutrophil infiltration.

Conclusions:
This study identified three distinct stroma types differentially associated with survival, immunity, and molecular features, thereby underscoring the importance of stromal heterogeneity in subtyping pancreatic cancers and supporting the development of antistromal therapies.
Serial Circulating Tumor DNA in Predicting and Monitoring the Effect of Neoadjuvant Chemoradiotherapy in Patients with Rectal Cancer: A Prospective Multicenter Study
Authors: Zhou Jiaolin , Wang Changxi , Lin Guole , Xiao Yi , Jia Wenzhuo , Xiao Gang , Liu Qian , Wu Bin , Wu Aiwen , Qiu Huizhong , Zhang Fuquan , Hu Ke , Xue Huadan , Shen Zhanlong , Wang Zhenjun , Han Jiagang , Niu Beizhan , Xu Yaping , Yu Zicheng , Yang Ling 
Published: October 2020

AbstractPurpose:We investigated the value of circulating tumor DNA (ctDNA) in predicting tumor response to neoadjuvant chemoradiotherapy (nCRT), monitoring tumor burden, and prognosing survival in patients with locally advanced rectal cancer (LARC).Experimental Design:This prospective multicenter trial recruited 106 patients with LARC for treatment with nCRT followed by surgery. Serial ctDNAs were analyzed by next-generation sequencing at four timepoints: at baseline, during nCRT, presurgery, and postsurgery.Results:In total, 1,098 mutations were identified in tumor tissues of the 104 patients being analyzed (median, seven mutations/patient). ctDNA was detected in 75%, 15.6%, 10.5%, and 6.7% of cases at the four timepoints, respectively. None of the 29 patients with pathologic complete response (ypCR) had preoperative ctDNA detected. The preoperative ctDNA-positive rate was significantly lower in the well-responded patients with pathologic tumor regression grade of ypCAP 0–1 than ypCAP 2–3 group (P &lt; 0.001), lower in ypCR than non-ypCR group (P = 0.02), and lower in pathologic T stage (ypT) 0–2 than ypT 3–4 group (P = 0.002). With a median follow-up of 18.8 months, 13 patients (12.5%) experienced distant metastasis. ctDNA positivity at all four timepoints was associated with a shorter metastasis-free survival (MFS; P &lt; 0.05). Multivariate analyses showed that the median variant allele frequency (VAF) of mutations in baseline ctDNA was a strong independent predictor of MFS (HR, 1.27; P &lt; 0.001).Conclusions:We show that ctDNA is a real-time monitoring indicator that can accurately reflect the tumor burden. The median VAF of baseline ctDNA is a strong independent predictor of MFS.
Phase I Study of Lysine-Specific Demethylase 1 Inhibitor, CC-90011, in Patients with Advanced Solid Tumors and Relapsed/Refractory Non-Hodgkin Lymphoma
Authors: Hollebecque Antoine , Salvagni Stefania , Plummer Ruth , Isambert Nicolas , Niccoli Patricia , Capdevila Jaume , Curigliano Giuseppe , Moreno Victor , Martin-Romano Patricia , Baudin Eric , Arias Marina , Mora Sheila , de Alvaro Juan , Di Martino Jorge , Parra-Palau Josep L. , Sánchez-Pérez Tania , Aronchik Ida , Filvaroff Ellen H. , Lamba Manisha , Nikolova Zariana , de Bono Johann S. 
Published: October 2020

Abstract

Purpose:
Lysine-specific demethylase 1 (LSD1) is implicated in multiple tumor types, and its expression in cancer stem cells is associated with chemoresistance. CC-90011 is a potent, selective, and reversible oral LSD1 inhibitor. We examined CC-90011 in advanced solid tumors and relapsed/refractory (R/R) non-Hodgkin lymphoma (NHL).

Patients and Methods:
CC-90011-ST-001 (NCT02875223; 2015-005243-13) is a phase I, multicenter, first-in-human dose-escalation study. Nine dose levels of CC-90011 (1.25–120 mg) given once per week were explored. Primary objectives were to determine safety, maximum tolerated dose (MTD), and/or recommended phase II dose (RP2D). Secondary objectives were to evaluate preliminary efficacy and pharmacokinetics.

Results:
Fifty patients were enrolled, 49 with solid tumors (27 neuroendocrine tumors/carcinomas) and 1 with R/R NHL. Median age was 61 years (range, 22–75). Patients received a median of three (range, 1–9) prior anticancer regimens. The RP2D was 60 mg once per week; the nontolerated dose (NTD) and MTD were 120 mg once per week and 80 mg once per week, respectively. Grade 3/4 treatment-related toxicities were thrombocytopenia (20%; an on-target effect unassociated with clinically significant bleeding), neutropenia (8%; in the context of thrombocytopenia at the highest doses), and fatigue (2%). The patient with R/R NHL had a complete response, currently ongoing in cycle 34, and 8 patients with neuroendocrine tumors/carcinomas had stable disease ≥6 months, including bronchial neuroendocrine tumors, kidney tumor, and paraganglioma.

Conclusions:
CC-90011 is well tolerated, with the RP2D established as 60 mg once per week. The MTD and NTD were determined to be 80 mg once per week and 120 mg once per week, respectively. Further evaluation of CC-90011 is warranted.
Use of Natural Language Processing to Improve Identification of Patients With Peripheral Artery Disease
Authors: Weissler E. Hope , Zhang Jikai , Lippmann Steven , Rusincovitch Shelley , Henao Ricardo , Jones W. Schuyler 
Published: October 2020

Background:
Peripheral artery disease (PAD) is underrecognized, undertreated, and understudied: each of these endeavors requires efficient and accurate identification of patients with PAD. Currently, PAD patient identification relies on diagnosis/procedure codes or lists of patients diagnosed or treated by specific providers in specific locations and ways. The goal of this research was to leverage natural language processing to more accurately identify patients with PAD in an electronic health record system compared with a structured data–based approach.

Methods:
The clinical notes from a cohort of 6861 patients in our health system whose PAD status had previously been adjudicated were used to train, test, and validate a natural language processing model using 10-fold cross-validation. The performance of this model was described using the area under the receiver operating characteristic and average precision curves; its performance was quantitatively compared with an administrative data–based least absolute shrinkage and selection operator (LASSO) approach using the DeLong test.

Results:

The median (SD) of the area under the receiver operating characteristic curve for the natural language processing model was 0.888 (0.009) versus 0.801 (0.017) for the LASSO-based approach alone (DeLong
P
<0.0001). The median (SD) of the area under the precision curve was 0.909 (0.008) versus 0.816 (0.012) for the structured data–based approach. When sensitivity was set at 90%, the precision for LASSO was 65% and the machine learning approach was 74%, while the specificity for LASSO was 41% and for the machine learning approach was 62%.

Conclusions:
Using a natural language processing approach in addition to partial cohort preprocessing with a LASSO-based model, we were able to meaningfully improve our ability to identify patients with PAD compared with an approach using structured data alone. This model has potential applications to both interventions targeted at improving patient care as well as efficient, large-scale PAD research.

Graphic Abstract:

A
graphic abstract
is available for this article.
Pedagogy and Social Critique in the Era of Fragmentation: A Collective Writing Experiment as cadavres exquis
Authors: Lazo Veronica Garcia , Locke Kirsten , Rupcich Nicolas , O’Connor Gabby , Yoon Caroline , Longley Alys 
Published: October 2020

Abstract
This is the result of a collaborative and creative experiment, a process in which six scholars—Garcia Lazo, Locke, Rupcich, O’Connor, Yoon and Longley—agreed to co-author an article through written and/or visual pieces of work. The emphasis taken in the article is to perform a methodology of fragmentation. The article is to be read as a series of ‘folds’, where collages or fragments of text are contained and while each fold is numbered, the reader is invited to read any fold in any order. Using fragmentation as method in writing also inspired our interpretation of a body of work made up of multiple ‘folds’ from the collaborative parlour game played by the surrealist movement. Known as cadavre exquis, surrealists enjoyed the strange juxtaposition created by each artist’s contribution as they drew part of a body onto a folded piece of paper without seeing the previous drawings in each fold. While often referred to in the context of psychoanalysis, we instead emphasise the fragmentation and hybridity of this form of collaboration in order to critique of universalising narratives about education (and writing) that we consider to be at odds with the post-capitalist realities of contemporary education and life.
Does Balance Dynamics Well Capture the Secondary Circulation and Spinup of a Simulated Hurricane?
Authors: Montgomery Michael T. , Persing John 
Published: October 2020

AbstractThis study investigates a claim made by Heng et al. in an article published in 2017 and intimated soon after in their article published in 2018 that axisymmetric “balanced dynamics can well capture the secondary circulation in the full-physics model” during hurricane spinup. Using output from a new, convection-permitting, three-dimensional numerical simulation of an intensifying hurricane, azimuthally averaged forcings of tangential momentum and heat are diagnosed to force an axisymmetric Eliassen balance model under strict balance conditions. The balance solutions are found, inter alia, to poorly represent the peak inflow velocity in the boundary layer and present a layer of relatively deep inflow extending well above the boundary layer in the high-wind-speed region of the vortex. Such a deep inflow layer, a hallmark of the classical spinup mechanism for tropical cyclones comprising the radial convergence of absolute angular momentum above the boundary layer, is not found in the numerical simulation during the period of peak intensification. These deficiencies are traced to the inability of the balance model to represent the nonlinear boundary layer spinup mechanism. These results are contrasted with a pseudobalance Eliassen formulation that improves the solution in some respects while sacrificing strict thermal wind balance. Overall, the quantitative results refute the Heng et al. claim and implicate the general necessity of the nonlinear boundary layer spinup mechanism to explain the spinup of a hurricane in realistic model configurations and in reality.
Nonlinear Forecast Error Growth of Rapidly Intensifying Hurricane Harvey (2017) Examined through Convection-Permitting Ensemble Assimilation of GOES-16 All-Sky Radiances
Authors: Minamide Masashi , Zhang Fuqing , Clothiaux Eugene E. 
Published: October 2020

AbstractThe dynamics and predictability of the rapid intensification (RI) of Hurricane Harvey (2017) were examined using convection-permitting initialization, analysis, and prediction from a cycling ensemble Kalman filter (EnKF) that assimilated all-sky infrared radiances from the Advanced Baseline Imager on GOES-16. The EnKF analyses were able to evolve the various scales of the radiance fields associated with Harvey close to those observed, including those associated with scattered individual convective cells before the onset of rapid intensification (RI) and the organized vortex-scale convective system during and after RI. This was true for more than 3 days of a continuous assimilation cycling. Deterministic forecasts initialized from the EnKF analyses captured the rapidly deepening intensity of Harvey more than 24 h prior to its onset. To explore the predictability of Harvey’s intensity during RI, ensemble probabilistic forecasts and sensitivity analyses were conducted. It was found that significant ensemble spread growth was induced by initial perturbations individually in either the wind or moisture fields. The nonlinear interactions between wind and moisture perturbations further limited the predictability of the intensification process of Harvey by increasing the uncertainty in the simulated wind and moisture distributions and modifying the convective activity and its feedback on vortex flow. This study highlights both the importance of better initializing the dynamic and moisture state variables simultaneously and the potential contribution of satellite all-sky radiance assimilation on constraining them and their associated convective activity that impacts RI of tropical cyclones.