bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exhaled VOCs can discriminate subjects with COVID-19 from healthy controls
Authors: Woollam Mark , Angarita-Rivera Paula , Siegel Amanda P , Kalra Vikas , Kapoor Rajat , Agarwal Mangilal 
Published: April 2022

Abstract
COVID-19 detection currently relies on testing by reverse transcription polymerase chain reaction (RT-PCR) or antigen testing. However, SARS-CoV-2 is expected to cause significant metabolic changes in infected subjects due to both metabolic requirements for rapid viral replication and host immune responses. Analysis of volatile organic compounds (VOCs) from human breath can detect these metabolic changes and is therefore an alternative to RT-PCR or antigen assays. To identify VOC biomarkers of COVID-19, exhaled breath samples were collected from two sample groups into Tedlar bags: negative COVID-19 (n = 12) and positive COVID-19 symptomatic (n = 14). Next, VOCs were analyzed by headspace solid phase microextraction coupled to gas chromatography-mass spectrometry. Subjects with COVID-19 displayed a larger number of VOCs as well as overall higher total concentration of VOCs (p < 0.05). Univariate analyses of qualified endogenous VOCs showed approximately 18% of the VOCs were significantly differentially expressed between the two classes (p < 0.05), with most VOCs upregulated. Machine learning multivariate classification algorithms distinguished COVID-19 subjects with over 95% accuracy. The COVID-19 positive subjects could be differentiated into two distinct subgroups by machine learning classification, but these did not correspond with significant differences in number of symptoms. Next, samples were collected from subjects who had previously donated breath bags while experiencing COVID-19, and subsequently recovered (COVID Recovered subjects (n = 11)). Univariate and multivariate results showed >90% accuracy at identifying these new samples as Control (COVID-19 negative), thereby validating the classification model and demonstrating VOCs dysregulated by COVID are restored to baseline levels upon recovery.
The significance of ophiomorpha trace fossils as key sedimentological parameters for paleoenvironment assessment – case example in Klias and Kudat Peninsulas, Sabah
Authors: Shamsuddin A.A.S , Jirin S. , Razak M.S.F.A. , Kadir M.F.A. , Harith Z.Z.T. , Ghani A.F.A. , Mubin M. 
Published: April 2022

Abstract
Trace fossils amongst other sedimentological features are one of the key sedimentological parameters commonly used to assess paleoenvironment. This paper discusses on the occurrence of trace fossil of ichnogenera Ophiomorpha observed in outcrops of Temburong and Belait formations around Klias and Kudat peninsulas. The burrows which are commonly observed at the outcrop sites belong to four ichnospecies: O. rudis, O. annulata, O. recta and O. nodosa. They are variably oriented from vertical to sub-vertical and horizontal, branched to unbranched. In Temburong Formation, O. rudis, O. annulata, O. recta ichnospecies were observed quite commonly which are associated with deep marine environment. Meanwhile, Ophiomorpha nodosa that typically related with shallow-marine trace fossils only observed in Belait Formations. Based on the trace fossil occurrence in conjunction with other sedimentological observations, the paleoenvironment assessment was further improved.
Improving accuracy and efficiency in elastic finite difference modelling
Authors: Ang Chin Tee , Ghosh Deva Prasad 
Published: April 2022

Abstract
Multicomponent technology has known to have a better imaging quality as compared to P-wave imaging. However, the cost of acquiring and processing the multicomponent data is more costly than P-wave imaging. Although P-wave imaging may have poorer imaging capability as compared to shear wave imaging, a good P-wave imaging can still be obtained if a good seismic modelling technique is used. Thus, this paper aims to enhance seismic modelling technique, in terms of accuracy, suppression of grid dispersion, and reduction in computation time. The finite difference (FD) technique is used as the modelling scheme, and the elastic modelling approach is used in this paper. The new method is applied on homogeneous model and synthetic data, and then compared to conventional FD modelling (4th order), higher order FD modelling (14th order), optimization of staggered grid coefficients such as least squares method and Wang & Liang’s method. The comparison will then be shown and discussed.
The effect of particle size towards resistivity and chargeability for groundwater interpretation
Authors: Malik Ahmad Khairul Abd , Madun Aziman , Dan Mohd Firdaus Md , Tajudin Saiful Azhar Ahmad , Talib Mohd Khaidir Abu , Azmi Mohammad Izzat Shaffiq , Noh Khairul Arifin Mohd , Joret Ariffuddin 
Published: April 2022

Abstract
The most reliable and common method of surveying the groundwater is the electrical resistivity tomography (ERT). ERT is a non-destructive method of groundwater surveying where the current is being injected into the ground and the value of the subsurface resistivity and chargeability are determined. Multiple factors may influence the results of the ERT, especially the mineralogy, soils, rocks and water content. In this study, the effects of particle size and moisture content are assessed towards the resistivity and chargeability value. The materials that are used to conduct the testing are obtained from quarry and river. The gravel size samples from quarry were varied from sample size retained at 37.5 mm, 28mm, 20mm, 11.2mm, 6.7mm, 5mm and 2.36mm. Meanwhile, the sand size samples from the river were varied from sample sieve size passing 2mm and retained at 1.18 mm, 0.85mm, 0.60mm, 0.43mm, 0.30mm, 0.20mm, 0.15mm and 0.063 mm sieve. The gravel and sand-sized particles were tested on a saturated condition. The device used for the experiment is Terrameter LS 2 and the setting used is C1C2P1P2 to conduct the resistivity and induced polarization tests. The resistivity value for the gravel ranges from 162.5 Ωm at its highest to 77.5 Ωm at its lowest. In a fully saturated condition, the resistivity value for the sand ranges from 121 Ωm at its highest to 86.1 Ωm at its lowest. The chargeability value for the gravel in a saturated condition ranges from 5.57 ms to 7.87 ms with decreasing particle size. The highest chargeability value for sand is 12.31 ms and the lowest is 2.04 ms in a fully saturated condition also in a decreasing size of particle size. The resistivity and chargeability for water used in this study are 101.7 Ωm and 0.41 ms, respectively. Keywords: Resistivity, Induced Polarization, Granite, Sand, Chargeability.
Geochemistry analysis of geothermal water in Tulabolo Timur, Sulawesi, Indonesia
Authors: Napu Siti Suhartini S. , Manyoe Intan Noviantari , Arifin Yayu Indriati 
Published: April 2022

Abstract
Gorontalo has several geothermal manifestations, such as Lombongo, Pangi, Libungo, Hungayono and Tulabolo Timur. Research on geothermal areas must be carried out to obtain surface and subsurface information, then the geothermal areas can be further developed. The purpose of this study was to analyse the geochemistry water of the geothermal water in Tulabolo Timur, Bone Bolango Regency, Gorontalo Province, Sulawesi, Indonesia. The research method is divided into field observations and laboratory analysis. Data processing using Atomic Absorption Spectrophotometer (AAS) for cation and anion test. Data processing using Picaro Water Isotope Analyzer for isotope test. Subsurface temperature is determined using the geothermometer Na-K Giggenbach formula. The results of this research show that the fluid type of Tulabolo Timur geothermal area is chloride and the origin of fluid is from deep reservoir. Geothermal fluid when it approaches the surface is not affected by surrounding rocks. Tulabolo Timur geothermal fluids are categorized in the upflow zone. Geothermal fluid when it reaches the surface is diluted with meteoric water. Meteoric water is infiltrated below the surface in the recharge area, which is located in the north and south of the study area. The subsurface temperature of Tulabolo Timur is included in the high-temperature system.
Tunable plasmon-induced transparency in graphene-based plasmonic waveguide for terahertz band-stop filters
Authors: Li Meiping , Shi Yanpeng , Liu Xiaoyu , Song Jinmei , Wang Xiaodong , Yang Fuhua 
Published: April 2022

Abstract
Terahertz (THz) tunable filters have great advantages in miniaturizing integrated and multiband communication systems. Here, THz band-stop filter with switchable single/double plasmon-induced transparency (PIT) based on metal-dielectric-metal waveguide consisting of a ring-stub cavity and two graphene ribbons (GRs) on stub sidewalls is proposed. The switchable characteristics of single and dual-PIT are investigated numerically and theoretically by the finite-difference time-domain and the radiating multi-oscillator theory, displaying good correspondence. The single-PIT is excited by the destructive interference between bright mode and dark mode, which possesses significant tunability of resonant frequency and transmission amplitude due to the existence of GRs. When independently regulating chemical potentials of GRs on the left and right sidewalls, the dual-PIT emerges. And the filter based on dual-PIT switches from single stopband to dual-stopband or even multi-stopband filtering. Besides, the band-stop filtering performance of the tunable PIT can be further optimized by increasing the number of ring-stub cavities. The tunable PIT in graphene-based plasmonic waveguide holds potential for THz multiband communications and subwavelength plasmonic devices, such as filters, switches, modulators.
Orbital angular momentum sidebands in second harmonic generation of a vortex beam by a nonlinear crystal with inhomogeneous refractive index
Authors: Ghavami Sabouri Saeed 
Published: April 2022

Abstract
The manipulation of the orbital angular momentum (OAM) spectrum in new wavelengths generated by frequency conversion has a wide range of applications in quantum information technology and modern communications. Here, the second harmonic generation of a vortex beam in a nonlinear crystal with an inhomogeneous refractive index is considered. It is shown that by using a segmented oven and generating a controllable temperature gradient along the thickness of the nonlinear crystal, a transverse phase mismatch can be induced in the vortex beam. Accordingly, the OAM spectrum of the vortex beam can be changed by generating new OAM components in the spectrum. Compared with the nonlinear Bragg diffraction method, the presented method has the advantage of longer interaction length and higher efficiency.
On the Legibility of Immigration Today
Authors: Huehls Mitchum 
Published: April 2022

Abstract
Claudia Sadowski-Smith’s The New Immigrant Whiteness: Race, Neoliberalism, and Post-Soviet Migration to the United States (2018) and Alexandra Perisic’s Precarious Crossings: Immigration, Neoliberalism, and the Atlantic (2019) present unique challenges to contemporary immigration discourse. Focusing on post-Soviet immigrants to the US, Sadowski-Smith explores the complicated role that whiteness plays for immigrants who look white but suffer similar economic precarity and material deprivation as non-white immigrants. Sadowski-Smith’s work complicates our understanding of white privilege and makes the specific precarities of the post-Soviet immigrant newly legible. The immigrants in Perisic’s study aren’t white, but she provocatively suggests that their racial, ethnic, and national specificity should not be the primary lens for understanding their immigrant experience. Instead, challenging the tendency to read contemporary immigration through the racialized, postcolonial logic of the Black Atlantic, Perisic emphasizes global neoliberalism and economic precarity as defining features of contemporary immigrant experience. Whereas Sadowski-Smith seeks to make post-Soviet immigrants legible to contemporary immigration discourse, Perisic observes the many ways that immigrants today strategically lean into and embrace precarity, effectively making themselves illegible and inassimilable to liberal values. Taken together, these two monographs advance our thinking about immigration in challenging and provocative ways.
The Influence of Processing Speed, Attention, and Inhibition on Texas Functional Living Scale Performance
Authors: Roye Scott , Linck John F , Hoffmeister Jordan , Copeland Christopher T 
Published: April 2022

Abstract

Objective
Attention, inhibition, and processing speed are related to functional decline among older adults. This study attempts to clarify the relationships between these cognitive factors and adaptive functioning.

Method
We examined relationships between attention, inhibition, and processing speed, with scores on the Texas Functional Living Scale (TFLS), a performance-based measure of daily functioning, in a mixed clinical sample of 530 older adults who were referred for an outpatient neuropsychological evaluation.

Results
The current study used a confirmatory factor analysis (CFA) to derive a three-factor cognitive model consisting of attention, inhibition, and processing speed. Results from a hierarchical regression, which included factor scores from the CFA, revealed that processing speed was the only significant predictor of TFLS performance when all three cognitive factors were included within a single model.

Conclusion
These results highlight the influence of processing speed as an important indicator of functional decline among a clinical population of older adults.
Simulation and annotation of global acronyms
Authors: Filimonov Maxim , Chopard Daphné , Spasić Irena 
Published: April 2022

AbstractMotivationGlobal acronyms are used in written text without their formal definitions. This makes it difficult to automatically interpret their sense as acronyms tend to be ambiguous. Supervised machine learning approaches to sense disambiguation require large training datasets. In clinical applications, large datasets are difficult to obtain due to patient privacy. Manual data annotation creates an additional bottleneck.ResultsWe proposed an approach to automatically modifying scientific abstracts to (i) simulate global acronym usage and (ii) annotate their senses without the need for external sources or manual intervention. We implemented it as a web-based application, which can create large datasets that in turn can be used to train supervised approaches to word sense disambiguation of biomedical acronyms.Availability and implementationThe datasets will be generated on demand based on a user query and will be downloadable from https://datainnovation.cardiff.ac.uk/acronyms/.
Targeting cyclin-dependent kinase 7—association between CDK7 and pMED1 expression in prostate cancer tissue
Authors: Paulsen Finn-Ole , Kang Duan , Becker Finn , Roth Doris , Joerg Vincent , Dreyer Eva , Roesch Marie C , Seidel Christoph , Merseburger Axel S , Kirfel Jutta , Sailer Verena , Offermann Anne , Perner Sven 
Published: April 2022

Abstract
Cyclin-dependent kinase (CDK) 7-mediated phosphorylation of Mediator-complex subunit 1 (MED1) enhances androgen receptor (AR) activity in prostate cancer (PCa). Hyperactive AR-signalling plays a key role for the development of castration resistance. Several CDK7 inhibitors are currently under investigation in Phase I/II trials addressing solid tumours, including PCa. Aim of this study was to characterize the CDK7/phospho-(p)MED1 axis in human tissue. Immunohistochemistry was performed on 595 PCa samples including 394 primary tumour foci obtained by radical prostatectomy (RP), 64 advanced or recurrent tumours obtained by palliative transurethral resection of the prostate (pTUR), 65 lymph node metastases (LNM), 35 distant metastases (DM) and 36 benign samples. CDK7 is expressed in 79.3% of PCa tissues and protein levels are significantly higher in LNM, pTUR and DM and lower in benign tissues compared to primary tumours. CDK7 and pMED1 expression show strong positive correlation. High expression of CDK7 associated with shorter 5-year biochemical recurrence-free-survival (63.0% vs. 85.0%) and reduced survival persists when adjusted for T-Stage, nodal status, resection boundaries, grade group and pre-operative prostate-specific antigen in multivariate Cox-regression (hazard ratio 4.30; 95% CI, 1.43 to 12,40, P = 0.007). High CDK7 and pMED1 levels correlate with nuclear AR expression. CDK7 positive tumours harbour higher Ki67 expression indices and show more frequently positive ERG (ETS-related gene)-status. In conclusion, CDK7 is frequently expressed in human PCa and predicts disease recurrence after RP. Therapeutical inhibition of CDK7 might be a promising approach in treatment of advanced PCa.
Attentional modulation of beta-power aligns with the timing of behaviorally relevant rhythmic sounds
Authors: Foldal Maja D , Leske Sabine , Blenkmann Alejandro O , Endestad Tor , Solbakk Anne-Kristin 
Published: April 2022

AbstractIt is largely unknown how attention adapts to the timing of acoustic stimuli. To address this, we investigated how hemispheric lateralization of alpha (7–13 Hz) and beta (14–24 Hz) oscillations, reflecting voluntary allocation of auditory spatial attention, is influenced by tempo and predictability of sounds. We recorded electroencephalography while healthy adults listened to rhythmic sound streams with different tempos that were presented dichotically to separate ears, thus permitting manipulation of spatial–temporal attention. Participants responded to stimulus-onset-asynchrony (SOA) deviants (−90 ms) for given tones in the attended rhythm. Rhythm predictability was controlled via the probability of SOA deviants per block. First, the results revealed hemispheric lateralization of beta-power according to attention direction, reflected as ipsilateral enhancement and contralateral suppression, which was amplified in high- relative to low-predictability conditions. Second, fluctuations in the time-resolved beta-lateralization aligned more strongly with the attended than the unattended tempo. Finally, a trend-level association was found between the degree of beta-lateralization and improved ability to distinguish between SOA-deviants in the attended versus unattended ear. Differently from previous studies, we presented continuous rhythms in which task-relevant and irrelevant stimuli had different tempo, thereby demonstrating that temporal alignment of beta-lateralization with attended sounds reflects top-down attention to sound timing.
Coronavirus Disease 2019 Vaccine Boosting in Previously Infected or Vaccinated Individuals
Authors: Shrestha Nabin K , Shrestha Priyanka , Burke Patrick C , Nowacki Amy S , Terpeluk Paul , Gordon Steven M 
Published: April 2022

Abstract

Background
The purpose of this study was to determine whether boosting previously infected or vaccinated individuals with a vaccine developed for an earlier variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) protects against the Omicron variant.

Methods
Employees of Cleveland Clinic, previously infected with or vaccinated against coronavirus disease 2019 (COVID-19) and working the day the Omicron variant was declared a variant of concern, were included. The cumulative incidence of COVID-19 was examined over 2 months during an Omicron variant surge. Protection provided by boosting was evaluated using Cox proportional hazards regression. Analyses were adjusted for time since proximate SARS-CoV-2 exposure.

Results
Among 39 766 employees, 8037 (20%) previously infected and the remaining previously vaccinated, COVID-19 occurred in 6230 (16%) during the study. Risk of COVID-19 increased with time since proximate SARS-CoV-2 exposure, and boosting protected those &gt;6 months since prior infection or vaccination. In multivariable analysis, boosting was independently associated with lower risk of COVID-19 among those vaccinated but not previously infected (hazard ratio [HR], .43; 95% confidence interval [CI], .41–.46) as well as those previously infected (HR, .66; 95% CI, .58–.76). Among those previously infected, receipt of 2 compared with 1 dose of vaccine was associated with higher risk of COVID-19 (HR, 1.54; 95% CI, 1.21–1.97).

Conclusions
Administering a COVID-19 vaccine not designed for the Omicron variant &gt;6 months after prior infection or vaccination protects against Omicron variant infection. There is no advantage to administering more than 1 dose of vaccine to previously infected persons.
Decolonizing Digital Methods
Authors: Bosch Tanja 
Published: April 2022

AbstractThe rapid growth of the Internet and social media platforms has increasingly made these central focus areas for media scholars around the world. Within the context of the broader framework of the movement towards decolonizing media and communication studies, this growth of digital methods raises key questions including: How are digital methods in these contexts currently being used and how might scholars begin to think about “decolonizing” these methods? What do digital methods look like in a context of the digital divide? This short commentary reflects on these questions to make an argument for the need to decolonize digital methods.
Harnessing feature extraction capacities from a pre-trained convolutional neural network (VGG-16) for the unsupervised distinction of aortic outflow velocity profiles in patients with severe aortic stenosis
Authors: Lachmann Mark , Rippen Elena , Rueckert Daniel , Schuster Tibor , Xhepa Erion , von Scheidt Moritz , Pellegrini Costanza , Trenkwalder Teresa , Rheude Tobias , Stundl Anja , Thalmann Ruth , Harmsen Gerhard , Yuasa Shinsuke , Schunkert Heribert , Kastrati Adnan , Joner Michael , Kupatt Christian , Laugwitz Karl Ludwig 
Published: April 2022

Abstract

Aims
Hypothesizing that aortic outflow velocity profiles contain more valuable information about aortic valve obstruction and left ventricular contractility than can be captured by the human eye, features of the complex geometry of Doppler tracings from patients with severe aortic stenosis (AS) were extracted by a convolutional neural network (CNN).

Methods and results
After pre-training a CNN (VGG-16) on a large data set (ImageNet data set; 14 million images belonging to 1000 classes), the convolutional part was employed to transform Doppler tracings to 1D arrays. Among 366 eligible patients [age: 79.8 ± 6.77 years; 146 (39.9%) women] with pre-procedural echocardiography and right heart catheterization prior to transcatheter aortic valve replacement (TAVR), good quality Doppler tracings from 101 patients were analysed. The convolutional part of the pre-trained VGG-16 model in conjunction with principal component analysis and k-means clustering distinguished two shapes of aortic outflow velocity profiles. Kaplan–Meier analysis revealed that mortality in patients from Cluster 2 (n = 40, 39.6%) was significantly increased [hazard ratio (HR) for 2-year mortality: 3; 95% confidence interval (CI): 1–8.9]. Apart from reduced cardiac output and mean aortic valve gradient, patients from Cluster 2 were also characterized by signs of pulmonary hypertension, impaired right ventricular function, and right atrial enlargement. After training an extreme gradient boosting algorithm on these 101 patients, validation on the remaining 265 patients confirmed that patients assigned to Cluster 2 show increased mortality (HR for 2-year mortality: 2.6; 95% CI: 1.4–5.1, P-value: 0.004).

Conclusion
Transfer learning enables sophisticated pattern recognition even in clinical data sets of limited size. Importantly, it is the left ventricular compensation capacity in the face of increased afterload, and not so much the actual obstruction of the aortic valve, that determines fate after TAVR.