bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinicopathological and prognostic value of lysyl oxidase expression in gastric cancer: a systematic review, meta-analysis and bioinformatic analysis
Authors: Jia Zirui , Gao Jiacheng , Wang Yuhang , Zhou Tingting , Zhang Xiangwen , Zu Guo 
Published: October 2022

AbstractThe association between the expression of Lysyl oxidase (LOX) and its clinicopathological parameters and prognosis in patients with gastric cancer (GC) is still disputed. We performed this meta-analysis and bioinformatics analysis to clarify the relationship between the expression and methylation level of LOX with its clinicopathological parameters and prognostic value. We applied odds ratios with a 95% confidence interval to study the associations between LOX expression and clinicopathological parameters and overall survival (OS) in GC patients. In addition, association analysis of promoter methylation levels and expression of LOX with its prognostic value was performed using the Cancer Genome Atlas (TCGA) and four Gene Expression Omnibus (GEO) datasets. The PRISMA 2020 checklist was used to guide the data extraction and analysis. This meta-analysis includes seven clinical studies with a total of 1435 GC patients. LOX expression was related to lymph node metastasis and tumor distant metastasis in GC patients, but not to gender, tumor differentiation, Lauren classification, or tumor depth of invasion. Patients with GC grouped in high-expression of LOX had a much worse OS than those in low-expression. In addition, TCGA and four GEO datasets with 1279 samples were included in the bioinformatics analysis. The bioinformatics analysis showed that patients with high LOX levels had poor OS; low levels of methylation at some cg sites in the LOX gene were strongly related to poor OS and PFS; and methylation levels of LOX are negatively correlated with advanced tumor stage. The conclusion from comprehensive DNA methylation and gene expression analysis supports LOX as a specific diagnostic and prognosis biomarker in GC. LOX expression was related to lymph node metastasis, tumor distant metastasis and poor prognosis in GC. Low methylation levels were related to advanced tumor stage and poor prognosis in GC. Integrative analysis supports LOX as a specific diagnostic and prognosis biomarker in GC.
SoloTE for improved analysis of transposable elements in single-cell RNA-Seq data using locus-specific expression
Authors: Rodríguez-Quiroz Rocío , Valdebenito-Maturana Braulio 
Published: October 2022

AbstractTransposable Elements (TEs) contribute to the repetitive fraction in almost every eukaryotic genome known to date, and their transcriptional activation can influence the expression of neighboring genes in healthy and disease states. Single cell RNA-Seq (scRNA-Seq) is a technical advance that allows the study of gene expression on a cell-by-cell basis. Although a current computational approach is available for the single cell analysis of TE expression, it omits their genomic location. Here we show SoloTE, a pipeline that outperforms the previous approach in terms of computational resources and by allowing the inclusion of locus-specific TE activity in scRNA-Seq expression matrixes. We then apply SoloTE to several datasets to reveal the repertoire of TEs that become transcriptionally active in different cell groups, and based on their genomic location, we predict their potential impact on gene expression. As our tool takes as input the resulting files from standard scRNA-Seq processing pipelines, we expect it to be widely adopted in single cell studies to help researchers discover patterns of cellular diversity associated with TE expression.
A framework for dissecting affinities of multidrug efflux transporter AcrB to fluoroquinolones
Authors: Vergalli Julia , Chauvet Hugo , Oliva Francesco , Pajović Jelena , Malloci Giuliano , Vargiu Attilio Vittorio , Réfrégiers Matthieu , Ruggerone Paolo , Pagès Jean-Marie 
Published: October 2022

AbstractSufficient concentration of antibiotics close to their target is key for antimicrobial action. Among the tools exploited by bacteria to reduce the internal concentration of antibiotics, multidrug efflux pumps stand out for their ability to capture and expel many unrelated compounds out of the cell. Determining the specificities and efflux efficiency of these pumps towards their substrates would provide quantitative insights into the development of antibacterial strategies. In this light, we developed a competition efflux assay on whole cells, that allows measuring the efficacy of extrusion of clinically used quinolones in populations and individual bacteria. Experiments reveal the efficient competitive action of some quinolones that restore an active concentration of other fluoroquinolones. Computational methods show how quinolones interact with the multidrug efflux transporter AcrB. Combining experiments and computations unveils a key molecular mechanism acting in vivo to detoxify bacterial cells. The developed assay can be generalized to the study of other efflux pumps.
High cooperativity coupling to nuclear spins on a circuit quantum electrodynamics architecture
Authors: Rollano Victor , de Ory Marina C. , Buch Christian D. , Rubín-Osanz Marcos , Zueco David , Sánchez-Azqueta Carlos , Chiesa Alessandro , Granados Daniel , Carretta Stefano , Gomez Alicia , Piligkos Stergios , Luis Fernando 
Published: October 2022

AbstractNuclear spins are candidates to encode qubits or qudits due to their isolation from magnetic noise and potentially long coherence times. However, their weak coupling to external stimuli makes them hard to integrate into circuit quantum electrodynamics architectures, the leading technology for solid-state quantum processors. Here, we study the coupling of 173Yb(III) nuclear spin states in an [Yb(trensal)] molecule to superconducting cavities. Experiments have been performed on magnetically dilute single crystals placed on the inductors of lumped-element LC superconducting resonators with characteristic frequencies spanning the range of nuclear and electronic spin transitions. We achieve a high cooperative coupling to all electronic and most nuclear [173Yb(trensal)] spin transitions, a necessary ingredient for the implementation of qudit protocols with molecular spins using a hybrid architecture.
Current wastewater treatment targets are insufficient to protect surface water quality
Authors: Jones Edward R. , Bierkens Marc F. P. , Wanders Niko , Sutanudjaja Edwin H. , van Beek Ludovicus P. H. , van Vliet Michelle T. H. 
Published: October 2022

AbstractThe quality of global water resources is increasingly strained by socio-economic developments and climate change, threatening both human livelihoods and ecosystem health. With inadequately managed wastewater being a key driver of deterioration, Sustainable Development Goal (SDG) 6.3 was established to halve the proportion of untreated wastewater discharged to the environment by 2030. Yet, the impact of achieving SDG6.3 on global ambient water quality is unknown. Addressing this knowledge gap, we develop a high-resolution surface water quality model for salinity as indicated by total dissolved solids, organic pollution as indicated by biological oxygen demand and pathogen pollution as indicated by fecal coliform. Our model includes a novel spatially-explicit approach to incorporate wastewater treatment practices, a key determinant of in-stream pollution. We show that achieving SDG6.3 reduces water pollution, but is still insufficient to improve ambient water quality to below key concentration thresholds in several world regions. Particularly in the developing world, reductions in pollutant loadings are locally effective but transmission of pollution from upstream areas still leads to water quality issues downstream. Our results highlight the need to go beyond the SDG-target for wastewater treatment in order to achieve the overarching goal of clean water for all.
Machine learning and deep learning applications in microbiome research
Authors: Hernández Medina Ricardo , Kutuzova Svetlana , Nielsen Knud Nor , Johansen Joachim , Hansen Lars Hestbjerg , Nielsen Mads , Rasmussen Simon 
Published: October 2022

AbstractThe many microbial communities around us form interactive and dynamic ecosystems called microbiomes. Though concealed from the naked eye, microbiomes govern and influence macroscopic systems including human health, plant resilience, and biogeochemical cycling. Such feats have attracted interest from the scientific community, which has recently turned to machine learning and deep learning methods to interrogate the microbiome and elucidate the relationships between its composition and function. Here, we provide an overview of how the latest microbiome studies harness the inductive prowess of artificial intelligence methods. We start by highlighting that microbiome data – being compositional, sparse, and high-dimensional – necessitates special treatment. We then introduce traditional and novel methods and discuss their strengths and applications. Finally, we discuss the outlook of machine and deep learning pipelines, focusing on bottlenecks and considerations to address them.
Age-Based Trends in Cognitive-Communication Management for Adults in Subacute Rehabilitation Following New Onset Traumatic Brain Injury
Authors: Shorland Joanna , Douglas Jacinta , O'Halloran Robyn 
Published: October 2022

Purpose:
Although traumatic brain injury (TBI) has a disproportionate impact on older adults, there has been limited inclusion of these individuals in post-TBI cognitive-communication research. This study was undertaken to compare demographic and injury characteristics, speech-language pathology input, and broad outcomes for younger and older adults admitted to inpatient rehabilitation following TBI.

Method:

A retrospective audit of first occasion adult TBI admissions in 2019 to inpatient rehabilitation in an Australian metropolitan subacute hospital was conducted via medical record data. Admissions were located using
International Statistical Classification of Diseases, Tenth Revision, Australian Modification (ICD-10-AM)
coding that aligned with TBI. Comparisons were made for younger (18–54 years) and older (≥ 55 years) adults.

Results:
A total of 114 admissions (51.75% older adults) were included. Patient age ranged between 18 and 90 years. Falls caused TBI in the majority of older adults, whereas transport-related accidents were the most common cause for younger adults. Age-based trends for intracranial injury were observed. Cognitive-communication difficulties were the most common speech-language pathology diagnosis with no significant difference in prevalence between younger and older adults. Age group was not significantly associated with length of stay or discharge home.

Conclusions:
The implications of injury-related trends for older adults on post-TBI cognitive-communication are poorly understood. This lack of information is problematic given the frequency of cognitive-communication difficulties in this population. Research into cognitive-communication following new onset TBI in older adults is crucial to support rehabilitation service provision and improve outcomes for older adults.
Physicochemical and biological evaluation of chondroitin sulphate calcium phosphate cements using tetracalcium phosphate nanorod and microparticle powders
Authors: Jahandideh Rahim , Behnamghader Aliasghar , Hesaraki Saeed 
Published: October 2022

AbstractTetracalcium phosphate (TTCP) is one of the main powder components in self‐setting calcium phosphate cements. In this study, two types of chondroitin sulphate calcium phosphate cements were prepared using nanoscale rod‐like (R‐TTCP) and conventional irregular shape (C‐TTCP) microscale powders. R‐TTCP and C‐TTCP powders were synthesized by reverse microemulsion chemical process and conventional thermal method, respectively. Adequate analyses and experiments such as XRD, FE‐SEM, setting time, porosity, compressive strength, degradation, bioactivity, cytotoxicity, and MG63 cell adhesion were conducted to illustrate physicochemical and resorbable cements specific properties. According to the results, both cements formed hydroxyapatite through the cementation process. The R‐TTCP cement revealed a slightly longer initial but no difference in final setting time, less compressive strength, higher porosity and better degradation behaviour compared to C‐TTCP one. Taking into consideration the initial porosity, the cement made from R‐TTCP powder presented more aptness to participate in ion exchange in SBF resulting to fill the 15% more initial porosity via the precipitation of hydroxyapatite mineral. From the biological point of view, analysis of cytotoxicity and MG63 osteoblastic‐cell behaviour proved that both the cements had good viability and proper cell adhesion and activity.
Neural network for determining an asteroid mineral composition from reflectance spectra
Authors: Korda David , Penttilä Antti , Klami Arto , Kohout Tomáš 
Published: October 2022

Context.Chemical and mineral compositions of asteroids reflect the formation and history of our Solar System. This knowledge is also important for planetary defence and in-space resource utilisation. In the next years, space missions will generate extensive spectral datasets from asteroids or planets with spectra that will need to be processed in real time.Aims.We aim to develop a fast and robust neural-network-based method for deriving the mineral modal and chemical compositions of silicate materials from their visible and near-infrared spectra. The method should be able to process raw spectra without significant pre-processing.Methods.We designed a convolutional neural network with two hidden layers for the analysis of the spectra, and trained it using labelled reflectance spectra. For the training, we used a dataset that consisted of reflectance spectra of real silicate samples stored in the RELAB and C-Tape databases, namely olivine, orthopyroxene, clinopyroxene, their mixtures, and olivine-pyroxene-rich meteorites.Results.We used the model on two datasets. First, we evaluated the model reliability on a test dataset where we compared the model classification with known compositional reference values. The individual classification results are mostly within 10 percentage-point intervals around the correct values. Second, we classified the reflectance spectra of S-complex (Q-type and V-type, also including A-type) asteroids with known Bus–DeMeo taxonomy classes. The predicted mineral chemical composition of S-type and Q-type asteroids agree with the chemical composition of ordinary chondrites. The modal abundances of V-type and A-type asteroids show a dominant contribution of orthopyroxene and olivine, respectively. Additionally, our predictions of the mineral modal composition of S-type and Q-type asteroids show an apparent depletion of olivine related to the attenuation of its diagnostic absorptions with space weathering. This trend is consistent with previous results of the slower pyroxene response to space weathering relative to olivine.Conclusions.The neural network trained with real silicate samples and their mixtures is applicable for a quantitative mineral evaluation of spectra of asteroids that are rich in dry silicates. The modal abundances and mineral chemistry of common silicates (olivine and pyroxene) can be derived with an accuracy better than 10 percentage points. The classification is fast and has a relatively small computer-memory footprint. Therefore, our code is suitable for processing large spectral datasets in real time.
Deep study of A399-401: Application of a wide-field facet calibration
Authors: de Jong J. M. G. H. J. , van Weeren R. J. , Botteon A. , Oonk J. B. R. , Brunetti G. , Shimwell T. W. , Cassano R. , Röttgering H. J. A. , Tasse C. 
Published: October 2022

Context. Diffuse synchrotron emission pervades numerous galaxy clusters, indicating the existence of cosmic rays and magnetic fields throughout the intra-cluster medium. The general consensus is that this emission is generated by shocks and turbulence that are activated during cluster merger events and cause a (re-)acceleration of particles to highly relativistic energies. Similar emission has recently been detected in megaparsec-scale filaments connecting pairs of premerging clusters. These instances are the first in which diffuse emission has been found outside of the main cluster regions.
Aims. We aim to examine the particle acceleration mechanism in the megaparsec-scale bridge between Abell 399 and Abell 401 and assess in particular whether the synchrotron emission originates from first- or second-order Fermi reacceleration. We also consider the possible influence of active galactic nuclei (AGNs).
Methods. To examine the diffuse emission and the AGNs in Abell 399 and Abell 401, we used deep (∼40 h) LOw-Frequency ARray (LOFAR) observations with an improved direction-dependent calibration to produce radio images at 144 MHz with a sensitivity of σ = 79 μJy beam−1 at a 5.9″ × 10.5″ resolution. Using a point-to-point analysis, we searched for a correlation between the radio and X-ray brightness from which we would be able to constrain the particle reacceleration mechanism.
Results. Our radio images show the radio bridge between the radio halos at high significance. We find a trend between the radio and X-ray emission in the bridge. We also measured the correlation between the radio and X-ray emission in the radio halos and find a strong correlation for Abell 401 and a weaker correlation for Abell 399. On the other hand, we measure a strong correlation for the radio halo extension from A399 in the northwest direction. With our deep images, we also find evidence for AGN particle injection and reenergized fossil plasma in the radio bridge and halos.
Conclusions. We argue that second-order Fermi reacceleration is currently the most favored process to explain the radio bridge. In addition, we find indications for a scenario in which past AGN particle injection might introduce significant scatter in the relation between the radio and X-ray emission in the bridge, but may also supply the fossil plasma needed for in situ reacceleration. The results for Abell 401 are also clearly consistent with a second-order Fermi reacceleration model. The relation between the thermal and nonthermal components in the radio halo in Abell 399 is affected by a recent merger. However, a strong correlation toward its northwest extension and the steep spectrum in the radio halo support an origin of the radio emission in a second-order Fermi reacceleration model as well. The evidence that we find for reenergized fossil plasma near Abell 399 and in the radio bridge supports the reacceleration of the fossil plasma scenario.
Trend Analysis of Global Web Searches (2004–2022) on Oral Cancer and Its Major Risk Factors
Authors: Kanmodi Kehinde Kazeem , Salami Afeez Abolarinwa , Nwafor Jacob Njideka , Olomo Charles Adetokunbo , Nnyanzi Lawrence Achilles 
Published: October 2022

Abstract
Background Oral cancer is the 15th leading cause of mortality globally. The Internet is an online source of information pertaining to oral cancer and its major risk factors. This study aims to analyze the trend of global online interest on oral cancer and its major risk factors through an analysis of web searches of oral cancer.
Materials and Methods This study analyzed the web searches conducted, from 2004 to January 2022, on oral cancer and its major risk factors (tobacco use, harmful alcohol use, and human papillomavirus [HPV] infection) using data obtained from Google Trends.
Results Within the time frame under study, oral cancer had multiple peak search periods, with the highest relative search volume index (SVI) for a period being 1; the peak search period for alcohol was March 2020 (SVI = 100); the peak search periods for tobacco were March to April 2004 (SVI = 17); and the peak search period of HPV was April 2004 (SVI = 1). Globally, alcohol was the most common searched term among these four terms (oral cancer, alcohol, tobacco, and HPV) except in Turkey where tobacco was the most common (55%) searched term. The top 25 search queries for oral cancer, HPV, tobacco, and alcohol had SVI ranges of 22 to 100, 12 to 100, 28 to 100, and 18 to 100, respectively. From these search queries, it was observed that people have interest in oral cancer symptomatology, and the adverse effects of tobacco, alcohol, and HPV.
Conclusion This study revealed an overall decline in the online interest on oral cancer and its major risk factors on a global scale.
Lunate Fracture Morphology in Kienbock's Disease—A Computed Tomography Study
Authors: MacLean Simon B. M. , Bain Gregory I. 
Published: October 2022

Abstract
Background The pathogenesis of Kienbock's disease is poorly understood. The coronal fracture line is acknowledged as a poor prognostic marker in the disease. Other fracture types in the Kienbock's wrist have subsequently been identified.
Questions/Purposes The aim is to study the fracture morphology of the lunate in a cohort of patients using computed tomography.
Methods Patient images were acquired using a set protocol with four-dimensional computed tomography scanning. Images were reviewed by two orthopaedic surgeons and a consultant radiologist. Static and dynamic images were assessed and a fracture map created. The relationship of fracture type to other parameters was then analyzed.
Results Twenty-three patients were included in the study, including 11 males and 12 females, with a mean age of 43 years. Total frequency of fracture lines in the cohort was coronal – 26, proximal subchondral bone plate type – 24, avulsion – 19, sagittal – 16, and distal subchondral bone plate type – 11. There were statistically significantly more proximal than distal subchondral bone plate fractures (p = 0.03), and more coronal fractures than distal subchondral bone plate fractures (p = 0.01). There were statistically significantly more radiolunate ligament-avulsion types (p <0.001) than other types. The sagittal fracture line through the lunate approximated closely to the ulnar edge of the capitate and the ulnar edge of the radius.
Conclusion Study on the fracture morphology in the Kienbock's wrist has improved our understanding of the disease pathogenesis. Fracture lines may correspond to loading points, intrinsic and extrinsic ligament avulsions. These fracture types may play a role in disease progression and are important to identify when considering lunate salvage surgery.
Raman tensor studies on defective non-van der Waals Bi2O2Se
Authors: Kim Un Jeong , Nam Seung Hyun , Kim Seok In , Han Yoojoong , Yoon Jeechan , Gutiérrez Humberto R. , Cheon Miyeon , Kim Gun Cheol , Park Yeonsang , Lee Moonsang , Hahm Myung Gwan , Son Hyungbin 
Published: October 2022

The Raman tensors of the three modes at ∼55, ∼80, and ∼160 cm−1 for the non-van der Waals layered material Bi2O2Se, which were assigned to Eu, Eg, and A1g, respectively, were experimentally investigated. Two modes at ∼55 and ∼80 cm−1, which were not observable in perfect crystal Bi2O2Se in the backscattering configuration, owing to the Raman selection rule, were activated by defects. These two modes exhibit strong polarization dependence at line defects and the excitation energy; thus, their Raman polarizability tensors exhibit strong dependence on the defect morphology and geometric characteristics of Bi2O2Se. The results of this study confirm that the Raman tensors of nanocrystalline structures can be modulated by defects.