bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic significance and oncogene function of cathepsin A in hepatocellular carcinoma
Authors: Wang Huaxiang , Xu Fengfeng , Yang Fang , Lv Lizhi , Jiang Yi 
Published: July 2021

AbstractCathepsin A (CTSA) is a lysosomal protease that regulates galactoside metabolism. The previous study has shown CTSA is abnormally expressed in various types of cancer. However, rarely the previous study has addressed the role of CTSA in hepatocellular carcinoma (HCC) and its prognostic value. To study the clinical value and potential function of CTSA in HCC, datasets from the Cancer Genome Atlas (TCGA) database and a 136 HCC patient cohort were analyzed. CTSA expression was found to be significantly higher in HCC patients compared with normal liver tissues, which was supported by immunohistochemistry (IHC) validation. Both gene ontology (GO) and The Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses demonstrated that CTSA co-expressed genes were involved in ATP hydrolysis coupled proton transport, carbohydrate metabolic process, lysosome organization, oxidative phosphorylation, other glycan degradation, etc. Survival analysis showed a significant reduction both in overall survival (OS) and recurrence-free survival (RFS) of patients with high CTSA expression from both the TCGA HCC cohort and 136 patients with the HCC cohort. Furthermore, CTSA overexpression has diagnostic value in distinguishing between HCC and normal liver tissue [Area under curve (AUC) = 0.864]. Moreover, Gene set enrichment analysis (GSEA) showed that CTSA expression correlated with the oxidative phosphorylation, proteasome, and lysosome, etc. in HCC tissues. These findings demonstrate that CTSA may as a potential diagnostic and prognostic biomarker in HCC.
Community structure and metabolic potentials of the traditional rice beer starter ‘emao’
Authors: Narzary Diganta , Boro Nitesh , Borah Ashis , Okubo Takashi , Takami Hideto 
Published: July 2021

AbstractThe emao, a traditional beer starter used in the North–East regions of India produces a high quality of beer from rice substrates; however, its microbial community structure and functional metabolic modules remain unknown. To address this gap, we have used shot-gun whole-metagenome sequencing technology; accordingly, we have detected several enzymes that are known to catalyze saccharification, lignocellulose degradation, and biofuel production indicating the presence of metabolic functionome in the emao. The abundance of eukaryotic microorganisms, specifically the members of Mucoromycota and Ascomycota, dominated over the prokaryotes in the emao compared to previous metagenomic studies on such traditional starters where the relative abundance of prokaryotes occurred higher than the eukaryotes. The family Rhizopodaceae (64.5%) and its genus Rhizopus (64%) were the most dominant ones, followed by Phaffomycetaceae (11.14%) and its genus Wickerhamomyces (10.03%). The family Leuconostocaceae (6.09%) represented by two genera (Leuconostoc and Weissella) was dominant over the other bacteria, and it was the third-highest in overall relative abundance in the emao. The comprehensive microbial species diversity, community structure, and metabolic modules found in the emao are of practical value in the formulation of mixed-microbial cultures for biofuel production from plant-based feedstocks.
MCM-2, Ki-67, and EGFR downregulated expression levels in advanced stage laryngeal squamous cell carcinoma
Authors: Vivatvakin Sarocha , Ratchataswan Thanaporn , Leesutipornchai Thiratest , Ruangritchankul Komkrit , Keelawat Somboon , Mahattanasakul Patnarin , Bongsebandhu-phubhakdi Saknan 
Published: July 2021

AbstractWe present the conceptual study investigated the capacity of minichromosome maintenance-2 (MCM-2), Ki-67, and epidermal growth factor receptor (EGFR) to assess the severity and progression of laryngeal squamous cell carcinoma (LSCC) disease and to study the correlations among these markers. A total of 30 patients with LSCC with immunohistochemistry (IHC) staining for MCM-2, Ki-67 and EGFR were examined. Mean expression levels of the three markers were evaluated for comparing between early and advanced stages of LSCC. The mean MCM-2, Ki-67, and EGFR expression levels were significantly decreased in advanced-stage compared with early-stage LSCC. Pearson correlation analysis showed a statistically significant correlation between the MCM-2 and Ki-67. Regarding subgroup analyses, MCM-2, Ki-67, and EGFR showed significant differences between early- and advanced-stage LSCC with non-recurrence, while for the recurrent subgroup LSCC, only MCM-2 revealed a significant difference between early- and advanced-stage LSCC. Altogether, these results support the role for downregulation of MCM-2, Ki-67 and EGFR in advanced-stage LSCC and correlation of MCM-2 and Ki-67 expressions that would be a promising strategy to predict prognosis of LSCC including severity and progression. We contextualize our findings and advocate the position of the biological markers, especially MCM-2, as an emerging evaluation tool for LSCC disease.
Invasion, establishment, and spread of invasive mosquitoes from the Culex coronator complex in urban areas of Miami-Dade County, Florida
Authors: Wilke André B. B. , Vasquez Chalmers , Cardenas Gabriel , Carvajal Augusto , Medina Johana , Petrie William D. , Beier John C. 
Published: July 2021

AbstractSpecies from the Culex coronator complex are Neotropical species and potential vectors of Saint Louis and West Nile viruses. Culex coronator was first described in Trinidad and Tobago in the early twentieth century and since then it has invaded and has been reported established in most countries of the Americas. Species from the Culex coronator complex were first detected in the United States in the state of Louisiana in 2004 and were subsequently detected in Florida in 2005, reaching Miami-Dade County in 2008. We hypothesize that species from the Cx. coronator complex are adapting to urban environments in Miami-Dade County, Florida, and are becoming more present and abundant in these areas. Therefore, our objective was to investigate the patterns of the presence and abundance of species from the Cx. coronator complex in the urban areas of Miami-Dade County. Here we used weekly data comprised of 32 CDC traps from 2012 to 2020 and 150 BG-Sentinel traps from 2016 to 2020. A total of 34,146 female mosquitoes from the Cx. coronator complex were collected, 26,138 by CDC traps and 8008 by BG-Sentinel traps. While the number of CDC traps that were positive was relatively constant at 26–30 positive traps per year, the number of positive BG-Sentinel traps varied substantially from 50 to 87 positive traps per year. Furthermore, the heat map and logistic general linear model for repeated measures analyses showed a significant increase in both the distribution and abundance of mosquitoes from the Cx. coronator complex, indicating that these species are becoming more common in anthropized habitats being able to thrive in highly urbanized areas. The increase in the distribution and abundance of species from the Cx. coronator complex is a major public health concern. The ability of species from the Cx. coronator complex to benefit from urbanization highlights the need to better understand the mechanisms of how invasive vector mosquito species are adapting and exploiting urban habitats.
Serum midkine as non-invasive biomarker for detection and prognosis of non-small cell lung cancer
Authors: Stern Louisa , Mueller Erik , Bellon Eugen , Reeh Matthias , Grotelueschen Rainer , Guengoer Cenap , Melling Nathaniel , Goetz Mara , Perez Daniel R. , Izbicki Jakob R. , Rawnaq-Möllers Tamina , Ghadban Tarik 
Published: July 2021

AbstractLung cancer continues to be the leading cause for cancer-related deaths in men and women worldwide. Sufficient screening tools enabling early diagnosis are essential to improve patient outcomes. The aim of this study was to evaluate serum midkine (S-MK) both as a diagnostic and prognostic biomarker in non-small cell lung cancer (NSCLC). This single-center analysis included 59 NSCLC patients counting 30 squamous cell cancers and 29 adenocarcinomas. Preoperative S-MK concentration was determined using ELISA. Patients were followed up to five years. S-MK was found to be significantly overexpressed in patients with NSCLC compared to healthy controls (p < 0.001). The discriminative power of S-MK to differentiate NSCLC subjects from controls was fairly high with an area under the receiver operating characteristic curve of 0.83 (p < 0.001). Optimal sensitivity of 92% and reasonable specificity of 68% was reached at a threshold of 416 pg/ml S-MK. Patients with high S-MK concentration showed a significantly shorter overall survival compared to patients with low S-MK expression (p < 0.05). In conclusion, S-MK is overexpressed in patients with NSCLC and serves as an independent prognostic factor for overall survival. S-MK may thus be considered as an additional non-invasive biomarker not only for NSCLC screening but also for outcome prediction.
Hydrogen bonding networks and cooperativity effects in the aqueous solvation of trimethylene oxide and sulfide rings by microwave spectroscopy and computational chemistry
Authors: Silva Weslley G. D. P. , van Wijngaarden Jennifer 
Published: July 2021

The intermolecular interactions responsible for the microsolvation of the highly flexible trimethylene oxide (TMO) and trimethylene sulfide (TMS) rings with one and two water (w) molecules were investigated using rotational spectroscopy (8–22 GHz) and quantum chemical calculations. The observed patterns of transitions are consistent with the most stable geometries of the TMO–w, TMO–(w)2, and TMS–w complexes at the B2PLYP-D3(BJ)/aug-cc-pVTZ level and were confirmed using spectra of the 18O isotopologue. Due to its effectively planar backbone, TMO offers one unique binding site for solvation, while water can bind to the puckered TMS ring in either an axial or equatorial site of the heteroatom. In all clusters, the first water molecule binds in the σv symmetry plane of the ring monomer and serves as a hydrogen bond donor to the heteroatom. The second water molecule is predicted to form a cooperative hydrogen bonding network between the three moieties. Secondary C–H⋯O interactions are a key stabilizing influence in trimers and also drive the preferred binding site in the TMS clusters with the axial binding site preferred in TMS–w and the equatorial form calculated to be more stable in the dihydrate. Using an energy partition scheme from the symmetry-adapted perturbation theory for the O, S, and Se containing mono- and dihydrates, the intermolecular interactions are revealed to be mainly electrostatic, but the dispersive character of the contacts is enhanced with the increasing size of the ring’s heteroatom due to the key role of longer-range secondary interactions.
Computing the Riemannian curvature of image patch and single-cell RNA sequencing data manifolds using extrinsic differential geometry
Authors: Sritharan Duluxan , Wang Shu , Hormoz Sahand 
Published: July 2021

Significance
High-dimensional datasets are becoming increasingly prevalent in many scientific fields. A universal theme connecting these high-dimensional datasets is the ansatz that data points are constrained to lie on nonlinear low-dimensional manifolds, whose structure is dictated by the natural laws governing the data. While tools have been developed for estimating global properties of these data manifolds, estimating the Riemannian curvature, a local property, has not been considered. Computing curvature of data manifolds offers both detailed criteria with which to evaluate models of these complex data (e.g., a Klein bottle model of image patches) and a way to explore detailed geometric features that cannot simply be visualized by the naked eye (e.g., in single-cell RNA-sequencing data).
Computational design of a synthetic PD-1 agonist
Authors: Bryan Cassie M. , Rocklin Gabriel J. , Bick Matthew J. , Ford Alex , Majri-Morrison Sonia , Kroll Ashley V. , Miller Chad J. , Carter Lauren , Goreshnik Inna , Kang Alex , DiMaio Frank , Tarbell Kristin V. , Baker David 
Published: July 2021

Significance
Programmed cell death protein-1 (PD-1) inhibitory antibodies, often referred to as checkpoint inhibitors, have revolutionized the treatment of cancer. However, there is an unmet need for PD-1 agonists to treat autoimmune disorders. Herein, we describe the de novo design of a small, stable PD-1 binding protein and development of a synthetic PD-1 agonist.
Translation of metaphorical idioms
Authors: Su Ke 
Published: July 2021

AbstractIdioms are one of the most problematic areas of translation. The difficulties in translating them largely come from their semantic opacity due to “the metaphorical use of the words they encompass” (Saeed 2017, 489). This study investigates the strategies used in the translation of metaphorical idioms, specifically idioms with stock metaphors, which have greater metaphorical force and more salient images than dead metaphors. The translation strategies were surveyed in the two English translations of the classic Chinese novel,Hongloumeng(Dream of the red chamber). The results show that the choice of strategies is influenced by the relationship between the source language and the target language, the source text’s status, and the translators’ specific approaches. The images in translated metaphorical idioms received special attention in terms of their removal, retention, and replacement. An analysis of the functions of strategies is also presented. The varied combinations of these strategies further attest to the difficulty in translating metaphorical idioms. Moreover, they also have a role in translators’ style and the effect of the target text.
Tracing trans-regional discursive flows in Pink Dot Hong Kong promotional videos
Authors: Rowlett Benedict J. L. , Go Christian 
Published: July 2021

AbstractIn this article, we extend discourse analytical research that has focused on Pink Dot events in Singapore to events in Hong Kong. As such we engage queer Sinophone perspectives to examine the simultaneously local and transregional epistemological flows that converge and diverge within the margins of the Sinophone cultural sphere. Using a multimodal analysis of two Pink Dot Hong Kong promotional videos, we investigate the extent to which these videos follow the (homo)normative and (homo)nationalist discursive strategies identified in the literature on Pink Dot Singapore. Our analysis suggests that ambivalences surrounding national identity, citizenship and state-sponsored national values in the Hong Kong videos bring into question readings of the Pink Dot movement as a (homo)nationalist enterprise, thus indicating an emergent relocalization of Pink Dot strategies that draws attention to how queer movements in Hong Kong are currently being shaped within the city’s broader sociopolitical context.
Ideological manoeuvres in and around Pink Dot
Authors: Lazar Michelle M. 
Published: July 2021

Abstract
This commentary comprises two parts. In the first part, different ways ‘ideological manoeuvres’ performed in and around
Pink Dot discourses in Singapore and Hong Kong, as evinced in this special issue, are highlighted. ‘Ideological manoeuvres’ refer to the
ideological actions and skilful management undertaken by social actors, explicitly or implicitly, to bring about or secure a tactical end in
support of, or in opposition to, the Pink Dot LGBT social movement. In the second part, how the ideological manoeuvres are on-goingly shaped
by, and shape, the geopolitics of gender/sexuality in Singapore and Hong Kong are discussed. In this regard, two areas are highlighted: the
politics of Pink Dot’s expressed apoliticism; and the transnational purchase of Pink Dot’s mode of political organising. Both of these areas
‘speak to’ a critical project on the decolonisation of gender/sexual knowledge-making and practice in these two Asian contexts.
Re-examining the role of mood selection type in Spanish heritage speakers’ subjunctive production
Authors: Perez-Cortes Silvia 
Published: July 2021

Abstract
Verbal morphology is a particularly vulnerable domain in the grammars of Spanish heritage speakers (HSs). Among
the most frequently studied phenomena is mood selection, identified as a pervasive locus of variability that affects the
production of subjunctive more prominently. The present article explores this area of research by examining the effects of mood
selection type on HSs’ subjunctive use. In contrast with previous studies, this investigation controls for propositional modality,
focusing its analyses on instances of obligatory and variable subjunctive selection within deontic predicates. Results from a
production task revealed that, despite the presence of between-group differences driven by participants’ levels of proficiency,
type of selection did not significantly modulate their rates of subjunctive use. These findings challenge previous claims about
the extent to which this factor affects Spanish HSs’ performance, and highlight the importance of considering propositional
modality when examining the acquisition of mood.
Multi-objective Optimization of Interferometric Array u–v Coverage
Authors: Zhang Rongyu , Yan Jingye , Wu Lin , Wu Ji 
Published: July 2021

Abstract
A new principle is introduced to optimize the configuration of an interferometric array, based on the trade-off between the uniform and Gaussian u–v distributions. The multi-objective optimization method, nondominated sorting genetic algorithm II (NSGA-II), is applied to achieve the optimal trade-off. The resulting array having a single configuration can meet the observation requirements of both compact and extended sources. This method has been successfully applied to design a 16-element array as the initial stage of the Daocheng Solar Radio Telescope to illustrate its feasibility. NSGA-II is improved by introducing artificial intervention into the genetic operator to solve the equality constraints. The improved NSGA-II is applied to obtain the Pareto optimal set, and a 16-element array configuration is retrieved with the best u–v trade-off between the snapshot mode and Earth rotation synthesis mode.
Eagle for better genome-wide association mapping
Authors: George Andrew W , Verbyla Arunas , Bowden Joshua 
Published: July 2021

Abstract
Eagle is an R package for multi-locus association mapping on a genome-wide scale. It is unlike other multi-locus packages in that it is easy to use for R users and non-users alike. It has two modes of use, command line and graphical user interface. Eagle is fully documented and has its own supporting website, http://eagle.r-forge.r-project.org/index.html. Eagle is a significant improvement over the method-of-choice, single-locus association mapping. It has greater power to detect SNP-trait associations. It is based on model selection, linear mixed models, and a clever idea on how random effects can be used to identify SNP-trait associations. Through an example with real mouse data, we demonstrate Eagle’s ability to bring clarity and increased insight to single-locus findings. Initially, we see Eagle complementing single-locus analyses. However, over time, we hope the community will make, increasingly, multi-locus association mapping their method-of-choice for the analysis of genome-wide association study data.
Combined video-assisted thoracoscopy surgery and posterior midline incision for en bloc resection of non-small-cell lung cancer invading the spine
Authors: Hireche Kheira , Moqaddam Mathieu , Lonjon Nicolas , Marty-Ané Charles , Solovei Laurence , Ozdemir Baris Ata , Canaud Ludovic , Alric Pierre 
Published: July 2021

Abstract

OBJECTIVES
This article aims to evaluate the feasibility and safety of a hybrid video-assisted thoracic surgery (VATS) approach to achieve en bloc lobectomy and spinal resection for non-small-cell lung cancer (NSCLC).

METHODS
Between October 2015 and November 2020, 10 patients underwent VATS anatomical lobectomy and en bloc chest wall and spinal resection through a limited posterior midline incision as a single operation for T4 (vertebral involvement) lung cancer. Nine patients had Pancoast syndrome without vascular involvement and 1 patient had NSCLC of the right lower lobe with invasion of T9 and T10.

RESULTS
There were 5 men and 5 women. The mean age was 61 years (range: 47–74 years). Induction treatment was administered to 9 patients (90%). The average operative time was 315.5 min (range: 250–375 min). The average blood loss was 665 ml (range: 100–2500 ml). Spinal resection was hemivertebrectomy in 6 patients and wedge corpectomy in 4 patients. Complete resection (R0) was achieved in all patients. The average hospitalization stay was 14 days (range: 6–50 days). There was no in-hospital mortality. The mean follow-up was 32.3 months (range: 6–66 months). Six patients (60%) are alive without recurrence.

CONCLUSIONS
VATS is feasible and safe to achieve en bloc resection of NSCLC inviding the spine without compromising oncological efficacy. Further experience and longer follow-up are needed to determine if this approach provides any advantages over thoracotomy.
Excess deaths reveal the true spatial, temporal and demographic impact of COVID-19 on mortality in Ecuador
Authors: Cuéllar Leticia , Torres Irene , Romero-Severson Ethan , Mahesh Riya , Ortega Nathaniel , Pungitore Sarah , Hengartner Nicolas , Ke Ruian 
Published: July 2021

Accepted

Background
In early 2020, Ecuador reported one of the highest surges of per capita deaths across the globe.

Methods
We collected a comprehensive dataset containing individual death records between 2015 and 2020, from the Ecuadorian National Institute of Statistics and Census and the Ecuadorian Ministry of Government. We computed the number of excess deaths across time, geographical locations and demographic groups using Poisson regression methods.

Results
Between 1 January and 23 September 2020, the number of excess deaths in Ecuador was 36 402 [95% confidence interval (CI): 35 762–36 827] or 208 per 100 000 people, which is 171% of the expected deaths in that period in a typical year. Only 20% of the excess deaths are attributable to confirmed COVID-19 deaths. Strikingly, in provinces that were most affected by COVID-19 such as Guayas and Santa Elena, the all-cause deaths are more than double the expected number of deaths that would have occurred in a normal year. The extent of excess deaths in men is higher than in women, and the number of excess deaths increases with age. Indigenous populations had the highest level of excess deaths among all ethnic groups.

Conclusions
Overall, the exceptionally high level of excess deaths in Ecuador highlights the enormous burden and heterogeneous impact of COVID-19 on mortality, especially in older age groups and Indigenous populations in Ecuador, which was not fully revealed by COVID-19 death counts. Together with the limited testing in Ecuador, our results suggest that the majority of the excess deaths were likely to be undocumented COVID-19 deaths.