bluuebunny/crossref_metadata_2025_split huggingface dataset:
183: MOLECULAR CHARACTERIZATION OF ESOPHAGEAL ADENOCARCINOMAS (EACS) AND ITS PROGNOSTIC IMPACT
Authors: Houlzé-Laroye C , Eveno C , Buisine M , Piessen G , Renaud F 
Published: April 2022

Abstract

Background and aim
Esophageal adenocarcinomas (EACs) have an increasing incidence and a poor prognosis. While gastric cancer molecular subtypes are well characterized with 4 categories: EBV+, Microsatellite instability (MSI), Genomically stable (GS), Chromosomal instability (CIN), there is less data available on EACs. Often compared to stomach, recent literature only describes CIN subtype in EACs, while our clinical experience suggests greater heterogeneity. The aims of our study were (i) to characterize EACs from a molecular perspective based on a large clinico-biological database and (ii) compare our clinico-pathological data with molecular results to analyze their prognostic impact.

Methods
516 patients underwent a transthoracic esophagectomy at the University Hospital of Lille. All HES staining slides from surgical specimen was reviewed, followed by a tissue microarrays analysis. Molecular subtypes were determined by immunohistochemistry (IHC) (MMR proteins for the deficient MMR (dMMR) and MSI-PCR for the dMMR/MSI subtype, E-cadherin for the GS subtype, HER2, C-MET and KRAS for the CIN subtype), and in situ hybridization (EBV+).

Results
In our series, 290 EACs are located on the esogastric junction (Siewert I and II), and 226 are above. Our current analysis highlighted one patient EBV+ and 26 dMMR status (9%). Interestingly, we observed discordances between MSI-PCR and IHC results in a third of cases (n = 8), suggesting possible modifications induced by pre-operative treatment. Our results about CIN and GS subtypes are consistent with literature with a loss of E-cadherin expression in 22 tumors (15%). An overexpression of HER2, C-MET and KRAS was noticed in 12 (8%), 41 (27%) and 13 (9%) tumors, respectively. We observed a trend toward better survival in the dMMR/MSI group comparing to GS subtype (90% vs 40% at 60 months, P = 0.07). Further analyses of the prognostic impact are in progress.

Conclusion
Our study highlights the presence of biomarkers in EACs, defining at least 4 molecular subtypes, partly overlapping to those already described in gastric cancer. Interestingly, finding of EBV+ and MSI tumors was unexpected and never described elsewhere in previous genomic characterization. The prognostic impact of these 4 subtypes underlined the necessity of routine molecular characterization to adapt the therapeutic strategy.
214: THE ADDITION OF ENDOSCOPIC ULTRASOUND AND PET IMAGING HAVE MINIMAL IMPACT ON DECISION-MAKING IN EARLY OESOPHAGEAL CANCER
Authors: Reyhani A , Dunn J , Baker C , Kelly M , Zeki S , Maisey N , Lagergren J , Gossage J , Davies A 
Published: April 2022

Abstract

Background and aim
With the increasing use of endoscopic mucosal resection (EMR) for the staging and management of early oesophageal cancer (EOC), the value of multiple staging investigations remains clear.

Methods
A single centre, ethically approved, prospective database of patients treated for EOC between 2000 and 2018 was analysed. This incorporated a transition period from oesophagectomy to endoscopic therapy as the treatment of choice for early cancers. Patients were staged with endoscopic ultrasound (EUS), Positron Emission Tomography (PET) and Computed Tomography (CT) with the accuracy and decision-making utility of these investigations assessed.

Results
In total 306 patients with glandular dysplasia or early adenocarcinoma were included (EMR n = 184; Surgery n = 113; EMR and Surgery n = 23). In patients treated by EMR staging patterns were similar for all modalities with low overall accuracy (Correct staging CT 40.1%, EUS 29.6%, PET 11%; Understaging CT 54.2%, EUS 51.9%, PET 82.9%; Overstaging CT 5.6%, EUS 18.5%, PET 6.1%). Incorrect overstaging that might have changed management occurred in 10 patients (3.6%) for T staging (T2) and 14 patients (5%) for N+. Similar staging inaccuracies persisted in both the surgery alone group and in those patients treated by oesophagectomy following EMR. Lymph node disease identified following surgery was rare (n = 8) and staging accuracy for these patients was low (CT 12.5%, EUS 12.5%, PET 0%).

Conclusion
In EOC, staging accuracy is low and the addition of EUS and PET change decision making in very few patients over and above standard CT. Factors predicting the need for surgery are predominantly obtained from the EMR histology rather than staging investigations. EUS and PET should only be used selectively in patients being assessed for EOC.
Sex-specific anthropometric and blood pressure trajectories and risk of incident atrial fibrillation: the Rotterdam Study
Authors: Lu Zuolin , Tilly Martijn J , Geurts Sven , Aribas Elif , Roeters van Lennep Jeanine , de Groot Natasja M S , Ikram M Arfan , van Rosmalen Joost , Kavousi Maryam 
Published: April 2022

Abstract

Aims
To investigate sex-specific longitudinal trajectories of various obesity-related measures and blood pressure at the population level and further assess the impact of these trajectories on new-onset atrial fibrillation (AF).

Methods and results
Participants with ≥2 repeated assessments for various risk factors from the population-based Rotterdam Study were included. Latent class linear mixed models were fitted to identify the potential classes. Cox proportional-hazard models were used to assess the association between risk factors’ trajectories and the risk of new-onset AF, with the most favourable trajectory as reference. Among 7367 participants (mean baseline age: 73 years, 58.8% women), after a median follow-up time of 8.9 years (interquartile range: 5.3–10.4), 769 (11.4%) participants developed new-onset AF. After adjustments for cardiovascular risk factors, persistent-increasing body mass index (BMI) trajectory carried a higher risk for AF [hazard ratio, 95% confidence interval: (1.39; 1.05–1.85) in men and (1.60; 1.19–2.15) in women], compared with the lower-and-stable BMI trajectory. Trajectories of elevated-and-stable waist circumference (WC) in women (1.53; 1.09–2.15) and elevated-and-stable hip circumference (HC) in men (1.83; 1.11–3.03) were associated with incident AF. For systolic blood pressure (SBP), the initially hypertensive trajectory carried the largest risk for AF among women (1.79; 1.21–2.65) and men (1.82; 1.13–2.95). Diastolic blood pressure trajectories were significantly associated with AF risk among women but not among men.

Conclusion
Longitudinal trajectories of weight, BMI, WC, HC, and SBP were associated with new-onset AF in both men and women. Diastolic blood pressure trajectories were additionally associated with AF in women. Our results highlight the importance of assessing long-term exposure to risk factors for AF prevention among men and women.
Ecological and Phenotypic Diversification after a Continental Invasion in Neotropical Freshwater Stingrays
Authors: Kolmann M A , Marques F P L , Weaver J C , Dean M N , Fontenelle J P , Lovejoy N R 
Published: April 2022

AbstractHabitat transitions are key potential explanations for why some lineages have diversified and others have not—from Anolis lizards to Darwin's finches. The ecological ramifications of marine-to-freshwater transitions for fishes suggest evolutionary contingency: some lineages maintain their ancestral niches in novel habitats (niche conservatism), whereas others alter their ecological role. However, few studies have considered phenotypic, ecological, and lineage diversification concurrently to explore this issue. Here, we investigated the macroevolutionary history of the taxonomically and ecologically diverse Neotropical freshwater river rays (subfamily Potamotrygoninae), which invaded and diversified in the Amazon and other South American rivers during the late Oligocene to early Miocene. We generated a time-calibrated, multi-gene phylogeny for Potamotrygoninae and reconstructed evolutionary patterns of diet specialization. We measured functional morphological traits relevant for feeding and used comparative phylogenetic methods to examine how feeding morphology diversified over time. Potamotrygonine trophic and phenotypic diversity are evenly partitioned (non-overlapping) among internal clades for most of their history, until 20–16 mya, when more recent diversification suggests increasing overlap among phenotypes. Specialized piscivores (Heliotrygon and Paratrygon) evolved early in the history of freshwater stingrays, while later trophic specialization (molluscivory, insectivory, and crustacivory) evolved in the genus Potamotrygon. Potamotrygonins demonstrate ecological niche lability in diets and feeding apparatus; however, diversification has mostly been a gradual process through time. We suggest that competition is unlikely to have limited the potamotrygonine invasion and diversification in South America.
US Supreme Court rules that unintentional mistakes of law, like mistakes of fact, may be considered under the copyright registration safe harbour provision
Authors: Macedo Charles R , Rothstein Chester , Goldberg David P , Lee Alice 
Published: April 2022

Abstract
On 24 February 2002, the US Supreme Court issued its decision in Unicolors, Inc. v H&M Hennes & Mauritz, LP, holding that an unintentional mistake of law is entitled to the benefit of the US Copyright Act’s safe harbour provision, § 411(b)(1)(A). In so doing, the Court clarified that not only unintentional mistakes of fact made during the application process, but also unintentional mistakes of law may be evaluated under the US Copyright Act’s safe harbour provision.
Detection and Isolation ofRickettsia tillamookensis(Rickettsiales: Rickettsiaceae) FromIxodes pacificus(Acari: Ixodidae) From Multiple Regions of California
Authors: Paddock Christopher D , Slater Kimetha , Swei Andrea , Zambrano Maria L , Kleinjan Joyce E , Padgett Kerry A , Saunders Megan E M , Andrews Elizabeth S , Trent Erin , Zhong Jianmin , Sambado Samantha , Goldsmith Cynthia S , Pascoe Emily L , Foley Janet , Lane Robert S , Karpathy Sandor E 
Published: April 2022

AbstractThe western black-legged tick (Ixodes pacificus) is the most frequently identified human-biting tick species in the western United States and the principal vector of at least three recognized bacterial pathogens of humans. A potentially pathogenic Rickettsia species, first described in 1978 and recently characterized as a novel transitional group agent designated as Rickettsia tillamookensis, also exists among populations of I. pacificus, although the distribution and frequency of this agent are poorly known. We evaluated DNA extracts from 348 host-seeking I. pacificus nymphs collected from 9 locations in five California counties, and from 916 I. pacificus adults collected from 24 locations in 13 counties, by using a real-time PCR designed specifically to detect DNA of R. tillamookensis. DNA of R. tillamookensis was detected in 10 (2.9%) nymphs (95% CI: 1.6–5.2%) and 17 (1.9%) adults (95% CI: 1.2–3.0%) from 11 counties of northern California. Although site-specific infection rates varied greatly, frequencies of infection remained consistently low when aggregated by stage, sex, habitat type, or geographical region. Four novel isolates of R. tillamookensis were cultivated in Vero E6 cells from individual adult ticks collected from Alameda, Nevada, and Yolo counties. Four historical isolates, serotyped previously as ‘Tillamook-like’ strains over 40 yr ago, were revived from long-term storage in liquid nitrogen and confirmed subsequently by molecular methods as isolates of R. tillamookensis. The potential public health impact of R. tillamookensis requires further investigation.
‘Quite a pleasant little afternoon’s sport’: Imperial Femininity and Hunting Culture in Impressions of a Tenderfoot
Authors: Molin Cherneski Kristina 
Published: April 2022

Abstract
This article examines the 1890 book Impressions of a Tenderfoot during a journey in search of sport in the Far West, by Susan MacKinnon St Maur. It argues that St Maur used conventions of male-produced texts on hunting and masculine notions of sport, while drawing on ‘feminine’ themes and topics as well, charting a unique ‘imperial femininity’ (Procida 2001). She proclaimed her ability to participate in male-coded outdoor activities, and argued for her place in the British Empire. Instead of obviously appropriating masculinity and challenging normative femininity, she found ways to make her exploits more palatable to her readers, while still asserting her status as a ‘sportsman’. Descriptions of the people she meets, whether settler or Indigenous, and her concern with race and the politics of imperialism, stress her place in the hierarchy of the colonial project, based on her own race and class, complicating normative gender roles of the period.
Evidence for neutron star triaxial free precession in Her X-1 from Fermi/GBM pulse period measurements
Authors: Kolesnikov Dmitry , Shakura Nikolai , Postnov Konstantin 
Published: April 2022

ABSTRACT
Her X-1/HZ Her is one of the best studied accreting X-ray pulsars. In addition to the pulsating and orbital periods, the X-ray and optical light curves of the source exhibit an almost periodic 35-d variability caused by a precessing accretion disc. The nature of the observed long-term stability of the 35-d cycle has been debatable. The X-ray pulse frequency of Her X-1 measured by the Fermi/GBM demonstrates periodical variations with X-ray flux at the main-on state of the source. We explain the observed periodic sub-microsecond pulse frequency changes by the free precession of a triaxial neutron star (NS) with parameters previously inferred from an independent analysis of the X-ray pulse evolution over the 35-d cycle. In the Fermi/GBM data, we identified several time intervals with a duration of half a year or longer where the NS precession period describing the pulse frequency variations does not change. We found that the NS precession period varies within one per cent in different intervals. Such variations in the free precession period on a year time-scale can be explained by $\lesssim 1{{\ \rm per\ cent}}$ changes in the fractional difference between the triaxial NS’s moments of inertia due to the accreted mass readjustment or variable internal coupling of the NS crust with the core.
A case of rheumatoid arthritis with bilateral shoulder bursitis accompanied by gas image
Authors: Kanayama Yoshiro , Tono Toshihiro , Tanaka Tomoki , Yamaoka Kunihiro 
Published: April 2022

ABSTRACT
We experienced a case of bilateral shoulder bursitis with gas images in a rheumatoid arthritis (RA) patient. A 60-year-old man with RA had been treated with weekly methotrexate 10 mg and daily prednisolone (PSL) 10 mg for 7 months. Generalized pain, especially in the bilateral shoulder joints, developed and exacerbated daily with increased C-reactive protein (CRP) level. Despite the initiation of biweekly sarilumab 200 mg, joint symptoms and CRP level continued to worsen. Computed tomography (CT) scan to determine the cause of severe shoulder inflammation revealed low absorption areas with contrast effects at the margins around the bilateral shoulder joints, accompanied by internal gas images. In addition, magnetic resonance imaging demonstrated subacromial bursae and coracoid bursae and bursitis, leading to the suspicion of abscess formation depending on the presence of gas image. In spite of antimicrobial therapy, arthralgia did not improve, and a CT-guided arthrocentesis of the left shoulder joint resulted in negative findings of infection in culture and pathological examinations. Switching treatment to intensive anti-inflammatory therapy with high-dose steroids and etanercept finally improved symptoms and CRP levels associated with the reduction of low absorption areas and disappearance of gas images at bilateral shoulder joints. Our case indicated that bursitis with gas image in RA patients involves unusual pathophysiology and requires intensive anti-rheumatic treatment.
George Balanchine’s Art of Choreographic Musicality in Tschaikovsky Pas de Deux
Authors: Leaman Kara Yoo 
Published: April 2022

Abstract
George Balanchine conceived ballets from music and, arguably, as music. This article uses a music-based notation system for dance to examine one complete piece, Variation 2 from Tschaikovsky Pas de Deux (1960). The transcription facilitates the application of music-analytic tools to choreomusical works. The analysis shows that Balanchine responded to musical features and applied musical techniques to dance, not only at the surface but at higher levels of form, creating choreomusical coherence. Performances by different dancers are compared in light of the analysis. This study offers a way to describe music-dance relationships using the tools and language of music analysis.
Antisense-mediated repression of SAGA-dependent genes involves the HIR histone chaperone
Authors: Soudet Julien , Beyrouthy Nissrine , Pastucha Anna Marta , Maffioletti Andrea , Menéndez Dario , Bakir Zahra , Stutz Françoise 
Published: April 2022

Abstract
Eukaryotic genomes are pervasively transcribed by RNA polymerase II (RNAPII), and transcription of long non-coding RNAs often overlaps with coding gene promoters. This might lead to coding gene repression in a process named Transcription Interference (TI). In Saccharomyces cerevisiae, TI is mainly driven by antisense non-coding transcription and occurs through re-shaping of promoter Nucleosome-Depleted Regions (NDRs). In this study, we developed a genetic screen to identify new players involved in Antisense-Mediated Transcription Interference (AMTI). Among the candidates, we found the HIR histone chaperone complex known to be involved in de novo histone deposition. Using genome-wide approaches, we reveal that HIR-dependent histone deposition represses the promoters of SAGA-dependent genes via antisense non-coding transcription. However, while antisense transcription is enriched at promoters of SAGA-dependent genes, this feature is not sufficient to define the mode of gene regulation. We further show that the balance between HIR-dependent nucleosome incorporation and transcription factor binding at promoters directs transcription into a SAGA- or TFIID-dependent regulation. This study sheds light on a new connection between antisense non-coding transcription and the nature of coding transcription initiation.
iFeatureOmega:an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets
Authors: Chen Zhen , Liu Xuhan , Zhao Pei , Li Chen , Wang Yanan , Li Fuyi , Akutsu Tatsuya , Bain Chris , Gasser Robin B , Li Junzhou , Yang Zuoren , Gao Xin , Kurgan Lukasz , Song Jiangning 
Published: April 2022

AbstractThe rapid accumulation of molecular data motivates development of innovative approaches to computationally characterize sequences, structures and functions of biological and chemical molecules in an efficient, accessible and accurate manner. Notwithstanding several computational tools that characterize protein or nucleic acids data, there are no one-stop computational toolkits that comprehensively characterize a wide range of biomolecules. We address this vital need by developing a holistic platform that generates features from sequence and structural data for a diverse collection of molecule types. Our freely available and easy-to-use iFeatureOmega platform generates, analyzes and visualizes 189 representations for biological sequences, structures and ligands. To the best of our knowledge, iFeatureOmega provides the largest scope when directly compared to the current solutions, in terms of the number of feature extraction and analysis approaches and coverage of different molecules. We release three versions of iFeatureOmega including a webserver, command line interface and graphical interface to satisfy needs of experienced bioinformaticians and less computer-savvy biologists and biochemists. With the assistance of iFeatureOmega, users can encode their molecular data into representations that facilitate construction of predictive models and analytical studies. We highlight benefits of iFeatureOmega based on three research applications, demonstrating how it can be used to accelerate and streamline research in bioinformatics, computational biology, and cheminformatics areas. The iFeatureOmega webserver is freely available at http://ifeatureomega.erc.monash.edu and the standalone versions can be downloaded from https://github.com/Superzchen/iFeatureOmega-GUI/ and https://github.com/Superzchen/iFeatureOmega-CLI/.
Heteroheptacene-based acceptors with thieno[3,2-b]pyrrole yield high-performance polymer solar cells
Authors: Luo Zhenghui , Ma Ruijie , Yu Jianwei , Liu Heng , Liu Tao , Ni Fan , Hu Jiahao , Zou Yang , Zeng Anping , Su Chun-Jen , Jeng U-Ser , Lu Xinhui , Gao Feng , Yang Chuluo , Yan He 
Published: April 2022

Abstract
Rationally utilizing and developing synthetic units is of particular significance for the design of high-performance non-fullerene small-molecule acceptors (SMAs). Here, a thieno[3,2-b]pyrrole synthetic unit was employed to develop a set of SMAs (ThPy1, ThPy2, ThPy3 and ThPy4) by changing the number or the position of the pyrrole ring in the central core based on a standard SMA of IT-4Cl, compared to which the four thieno[3,2-b]pyrrole-based acceptors exhibit bathochromic absorption and upshifted frontier orbital energy level due to the strong electron-donating ability of pyrrole. As a result, the polymer solar cells (PSCs) of the four thieno[3,2-b]pyrrole-based acceptors yield higher open-circuit voltage and lower energy loss relative to those of the IT-4Cl-based device. What is more, the ThPy3-based device achieves a power conversion efficiency (PCE) (15.3%) and an outstanding fill factor (FF) (0.771) that are superior to the IT-4Cl-based device (PCE = 12.6%, FF = 0.758). The ThPy4-based device realizes the lowest energy loss and the smallest optical band gap, and the ternary PSC device based on PM6:BTP-eC9:ThPy4 exhibits a PCE of 18.43% and a FF of 0.802. Overall, this work sheds light on the great potential of thieno[3,2-b]pyrrole-based SMAs in realizing low energy loss and high PCE.
A K+-sensitive AND-gate dual-mode probe for simultaneous tumor imaging and malignancy identification
Authors: Wang Qiyue , Li Fangyuan , Liang Zeyu , Liao Hongwei , Zhang Bo , Lin Peihua , Liu Xun , Hu Shen , Lee Jiyoung , Ling Daishun 
Published: April 2022

Abstract
Although molecular imaging probes have the potential to non-invasively diagnose a tumor, imaging probes that can detect a tumor and simultaneously identify tumor malignancy remain elusive. Here, we demonstrate a potassium ion (K+) sensitive dual-mode nanoprobe (KDMN) for non-invasive tumor imaging and malignancy identification, which operates via a cascaded ‘AND’ logic gate controlled by inputs of magnetic resonance imaging (MRI) and fluorescence imaging (FI) signals. We encapsulate commercial K+ indicators into the hollow cavities of magnetic mesoporous silica nanoparticles, which are subsequently coated with a K+-selective membrane that exclusively permits the passage of K+ while excluding other cations. The KDMN can readily accumulate in tumors and enhance the MRI contrast after systemic administration. Spatial information of the tumor lesion is thus accessible via MRI and forms the first layer of the ‘AND’ gate. Meanwhile, the KDMN selectively captures K+ and prevents interference from other cations, triggering a K+-activated FI signal as the second layer of the ‘AND’ gate in the case of a malignant tumor with a high extracellular K+ level. This dual-mode imaging approach effectively eliminates false positive or negative diagnostic results and allows for non-invasive imaging of tumor malignancy with high sensitivity and accuracy.