bluuebunny/crossref_metadata_2025_split huggingface dataset:
Examination of limonene concentrations using tapered plastic optical fiber sensors
Authors: Anbalagan Thanigai , Haroon Hazura , Rahim Hazli Rafis Abdul , Johari Siti Halma 
Published: December 2022

Abstract
A tapered plastic optic fiber (POF) was developed and demonstrated for monitoring different concentrations of limonene. The working mechanism of the sensor was dependent on the evanescent field interaction between light and the POF tapered region. The tapered POF was fabricated using a polishing-etching method to accomplish different waist diameters of 0.7 mm, 0.65 mm, 0.6 mm, 0.55 mm, and 0.5 mm in a 2 cm sensing region. The experiment was carried out with a blue LED with a wavelength of 400 nm and the output voltage was observed. As the concentration of the limonene solutions increased from 20% to 40%, 60%, 80%, and 100%, the refractive index also increased to 1.39, 1.41, 1.43, 1.44, and 1.47, respectively. The sensitivity of the sensor increased as the tapered waist diameter was reduced. The key benefits of this sensor are its ease of handling and fabrication in comparison to other types of sensors.
Performance of copper and palladium metal-semiconductor Schottky diode for optoelectronics
Authors: Zheng Kevin Ooi , Halim Mohd Mahadi 
Published: December 2022

Abstract
The growth of ZnO nanorods (NRs) have been performed by chemical bath deposition (CBD) method on ITO glass substrate. The optical properties along with the structural of ZnO NRs were studies by Field Emission Scanning Electron Microscope (FESEM), energy-dispersive X-ray (EDX), X-Ray Diffraction (XRD), and UV-Visible (UV-Vis) analysis. A 100 nm of Cu metal and Pd metal were deposited on top of synthesized ZnO NRs via sputtering. The electrical properties including I-V characteristics, rectifying ratio, Schottky Barrier Height (SBH) and ideality factor were investigated. Difference in work function for both metals resulting in different I-V characteristics, hence different value of rectifying ratio, SBH and ideality factor. The Cu sample possessed rectifying ratio, SBH and ideality factor of 1.07, 0.66 eV and 6.1 respectively, while Pd sample exhibits 87.84, 0.43 eV and 5 respectively. These intriguing values made possible for these metals to potentially serve as contact for ZnO-based optoelectronics devices, e.g LED, and random laser.
Squeezing over Two Octaves of Frequency Difference with Second Harmonic Coupling
Authors: Julius R , Ibrahim A-B M A 
Published: December 2022

Abstract
Using the quasiprobability positive P of phase space representation, we examine the features of squeezing over two octaves of frequency difference with each octave integrating two-channel nonlinear waveguides. The second harmonic coupling of the light fields is taken into account in the current arrangement. We discovered that single-mode squeezing is decreased by second harmonic coupling.
Pd single atom supported on N-doped egg tray graphene as formic acid dehydrogenation catalysts
Authors: Liu Cheng , Liu Wei , Miao Mao-sheng , Liu Jing-yao 
Published: December 2022

Abstract
Graphene and many 2D carbon allotropes are good support materials for single-atom catalysts (SACs) and have been successfully applied to many catalytic reactions. Herein, based on the egg tray graphene (ETG), a carbon allotrope constructed in our previous report, we designed ETG and three N-doped ETG supported Pd SACs, Pd@ETG-N
x
(x= 0–3), for dehydrogenation of formic acid (HCOOH) by density functional theory. Our calculations show that ETG is easier for N doping than graphene, and Pd single atom can be stably adsorbed on the ETG with different N doping concentrations. Major pathways of formic acid dehydrogenation and dehydration were identified. We found that HCOOH dehydrogenation proceeds along the COOH-mediated pathway on each catalyst. With the increased N content in the substrate, the activity and H2 selectivity of Pd SACs are greatly improved. Especially, among these four SACs, Pd@ETG-N3 shows the best catalytic performance, which is even better than Pd(111). Furthermore, electronic analysis was made to reveal the metal-support interactions and the origin of the activity trend of Pd@ETG-N
x
. Our study reveals the unique potential of carbon allotropes in catalyst design, and provides theoretical insights for rational design of efficient catalysts by adjusting the support and the coordination environment.
Molecular dynamics study on the mechanical properties of nanocrystalline Ni-W alloys with bimodal structure
Authors: Li Guo , Wang Ruipeng , Cai Qixing , Zhang Feng , Zhu Dasheng , Li Fengtian 
Published: December 2022

Abstract
In order to study the effects of coarse grain size and Ni content on the mechanical properties, the molecular dynamics (MD) simulation of nanocrystalline (NC) Ni-W alloys with bimodal structure is carried out. The bimodal NC Ni-W alloys samples are established by embedding coarse grain into the fine grain matrix. The solute Ni atoms in the alloys are segregated in the grain boundary affected zone (GBAZ) through severe plastic deformation (SPD). The uniaxial tensile simulation of the samples shows that the coarse grain size and Ni content have obvious effects on the mechanical properties of bimodal NC Ni-W alloys. The dislocation activities and deformation mechanism of the NC Ni-W alloys are discussed in detail by observing the atomic configurations and strain evolutions diagrams obtained by MD simulation. At the same time, the phenomenon of Hall-Petch relationship and inverse Hall-Petch relationship is also observed in the research process.
Comparing the Accuracy of Diagnostic Tests When Disease Is Characterized by an Ordinal Scale
Authors: Obuchowski Nancy A 
Published: December 2022

AbstractIn diagnostic medicine, the true disease status of a patient is often represented on an ordinal scale—for example, cancer stage (0, I, II, III, or IV) or coronary artery disease severity measured using the Coronary Artery Disease Reporting and Data System (CAD-RADS) scale (none, minimal, mild, moderate, severe, or occluded). With advances in quantitation of diagnostic images and in artificial intelligence (AI), both supervised and unsupervised algorithms are being developed to help physicians correctly grade disease. Most of the diagnostic accuracy literature deals with binary disease status (disease present or absent); however, tests diagnosing ordinal-scaled diseases should not be reduced to a binary status just to simplify diagnostic accuracy testing. In this paper, we propose different characterizations of ordinal-scale accuracy for different clinical use scenarios, along with methods for comparing tests. In the simplest scenario, just the proportion of correct grades is considered; other scenarios address the magnitude and direction of misgrading; and at the other extreme, a weighted accuracy measure with weights based on the relative costs of different types of misgrading is presented. The various scenarios are illustrated using a coronary artery disease example where the accuracy of AI algorithms in providing patients with the correct CAD-RADS grade is assessed.
Does Alcohol Withdrawal Influence Arterial Stiffness and Classical Risk Factors for Cardiovascular Disease for Persons With Alcohol Use Disorder?
Authors: Szołtysek-Bołdys Izabela , Zielińska-Danch Wioleta , Sarecka-Hujar Beata , Słodczyk-Mańkowska Ewa , Kozar-Konieczna Aleksandra , Sobczak Andrzej 
Published: December 2022

AbstractAimsThe amount and pattern of cigarette and alcohol consumption are highly associated with cardiovascular risk. The aim of the present study was the assessment of changes in arterial stiffness and classical risk factors for cardiovascular disease after alcohol withdrawal and detoxification in persons with alcohol use disorder.MethodsTwo hundred and forty-one individuals (men and women) participated in the investigation. The photoplethysmographic method was applied to assess arterial stiffness in three stages within 6 weeks. Participants were divided into subgroups based on age and sex. Analyses were performed using analysis of variance with repeated measures.ResultsDifferent variations in time of stiffness index (SI) and reflection index (RI) values were recorded. Some increases in triglycerides, total cholesterol, low-density lipoprotein and a decrease in high-density lipoproteins were observed in all analyzed groups. Both systolic and diastolic blood pressure (DP) changed significantly during the 3 weeks of the study only in a group of younger men. The SI is correlated with age and gender. No correlation of RI with sex was found; however, RI was strongly correlated with age, pulse and DP.ConclusionsThe presented study shows that some groups of patients (older women and younger men) after detoxification may be particularly vulnerable to vascular system disorders, i.e. arterial stiffness, making it suggested to include additional observation during therapy.
Aesthetic Implantation of Calcium Hydroxylapatite Does Not Interfere With Radiological Assessment of Bones in the Dorsum of the Hands
Authors: Moradi Amir , Ðaković Rada , Odena Gemma 
Published: December 2022

Abstract

Background
Calcium hydroxylapatite (CaHA) is a radiopaque dermal filler used to provide volume correction in the dorsum of the hand.

Objectives
The aim of this study was to evaluate whether CaHA implantation in the dorsum of the hand interferes with radiological assessment by obscuring the bones.

Methods
This 2-year, prospective, single-center, open-label study enrolled 20 subjects with Merz Hand Grading Scale (MHGS) grades ranging from moderate (MHGS 2 or 3; n = 10) to very severe (MHGS 4; n = 10). All subjects received an initial CaHA treatment and were offered up to 3 retreatments to provide volume correction in the dorsum of the hands, over a period of 18 months. Bone obscuration was assessed by blinded, licensed radiologists responsible for interpreting plain radiographs (X-rays).

Results
CaHA was seen to be present in 100% of hands in Month 1 X-rays and in 83.3% in Month 24 X-rays, but no bone obscuration was reported in any X-rays at any evaluated time point.

Conclusions
According to blinded radiologists, treatment with CaHA in the dorsum of the hand does not obscure radiographic assessment of the bones seen on X-rays up to 24 months after initial injection. The safety of CaHA retreatment was also demonstrated by the lack of bone obscuration after multiple retreatments.
Photoperiod and rainfall are associated with seasonal shifts in social structure in a songbird
Authors: Welklin Joseph F , Lantz Samantha M , Khalil Sarah , Moody Nicole M , Karubian Jordan , Webster Michael S 
Published: December 2022

Abstract
Seasonally breeding animals often exhibit different social structures during non-breeding and breeding periods that coincide with seasonal environmental variation and resource abundance. However, we know little about the environmental factors associated with when seasonal shifts in social structure occur. This lack of knowledge contrasts with our well-defined knowledge of the environmental cues that trigger a shift to breeding physiology in seasonally breeding species. Here, we identified some of the main environmental factors associated with seasonal shifts in social structure and initiation of breeding in the red-backed fairywren (Malurus melanocephalus), an Australian songbird. Social network analyses revealed that social groups, which are highly territorial during the breeding season, interact in social “communities” on larger home ranges during the non-breeding season. Encounter rates among non-breeding groups were related to photoperiod and rainfall, with shifting photoperiod and increased rainfall associated with a shift toward territorial breeding social structure characterized by reductions in home range size and fewer encounters among non-breeding social groups. Similarly, onset of breeding was highly seasonal and was also associated with non-breeding season rainfall, with greater rainfall leading to earlier breeding. These findings reveal that for some species, the environmental factors associated with the timing of shifts in social structure across seasonal boundaries can be similar to those that determine timing of breeding. This study increases our understanding of the environmental factors associated with seasonal variation in social structure and how the timing of these shifts may respond to changing climates.
Comprehensive investigation of pathway enrichment methods for functional interpretation of LC–MS global metabolomics data
Authors: Lu Yao , Pang Zhiqiang , Xia Jianguo 
Published: December 2022

Abstract
Background: Global or untargeted metabolomics is widely used to comprehensively investigate metabolic profiles under various pathophysiological conditions such as inflammations, infections, responses to exposures or interactions with microbial communities. However, biological interpretation of global metabolomics data remains a daunting task. Recent years have seen growing applications of pathway enrichment analysis based on putative annotations of liquid chromatography coupled with mass spectrometry (LC–MS) peaks for functional interpretation of LC–MS-based global metabolomics data. However, due to intricate peak-metabolite and metabolite-pathway relationships, considerable variations are observed among results obtained using different approaches. There is an urgent need to benchmark these approaches to inform the best practices. Results: We have conducted a benchmark study of common peak annotation approaches and pathway enrichment methods in current metabolomics studies. Representative approaches, including three peak annotation methods and four enrichment methods, were selected and benchmarked under different scenarios. Based on the results, we have provided a set of recommendations regarding peak annotation, ranking metrics and feature selection. The overall better performance was obtained for the mummichog approach. We have observed that a ~30% annotation rate is sufficient to achieve high recall (~90% based on mummichog), and using semi-annotated data improves functional interpretation. Based on the current platforms and enrichment methods, we further propose an identifiability index to indicate the possibility of a pathway being reliably identified. Finally, we evaluated all methods using 11 COVID-19 and 8 inflammatory bowel diseases (IBD) global metabolomics datasets.
Personalized immune subtypes based on machine learning predict response to checkpoint blockade in gastric cancer
Authors: Huang Weibin , Zhang Yuhui , Chen Songyao , Yin Haofan , Liu Guangyao , Zhang Huaqi , Xu Jiannan , Yu Jishang , Xia Yujian , He Yulong , Zhang Changhua 
Published: December 2022

Abstract
Immune checkpoint inhibitors (ICI) show high efficiency in a small fraction of advanced gastric cancer (GC). However, personalized immune subtypes have not been developed for the prediction of ICI efficiency in GC. Herein, we identified Pan-Immune Activation Module (PIAM), a curated gene expression profile (GEP) representing the co-infiltration of multiple immune cell types in tumor microenvironment of GC, which was associated with high expression of immunosuppressive molecules such as PD-1 and CTLA-4. We also identified Pan-Immune Dysfunction Genes (PIDG), a conservative PIAM-derivated GEP indicating the dysfunction of immune cell cooperation, which was associated with upregulation of metastatic programs (extracellular matrix receptor interaction, TGF-β signaling, epithelial-mesenchymal transition and calcium signaling) but downregulation of proliferative signalings (MYC targets, E2F targets, mTORC1 signaling, and DNA replication and repair). Moreover, we developed ‘GSClassifier’, an ensemble toolkit based on top scoring pairs and extreme gradient boosting, for population-based modeling and personalized identification of GEP subtypes. With PIAM and PIDG, we developed four Pan-immune Activation and Dysfunction (PAD) subtypes and a GSClassifier model ‘PAD for individual’ with high accuracy in predicting response to pembrolizumab (anti-PD-1) in advance GC (AUC = 0.833). Intriguingly, PAD-II (PIAMhighPIDGlow) displayed the highest objective response rate (60.0%) compared with other subtypes (PAD-I, PIAMhighPIDGhigh, 0%; PAD-III, PIAMlowPIDGhigh, 0%; PAD-IV, PIAMlowPIDGlow, 17.6%; P = 0.003), which was further validated in the metastatic urothelial cancer cohort treated with atezolizumab (anti-PD-L1) (P = 0.018). In all, we provided ‘GSClassifier’ as a refined computational framework for GEP-based stratification and PAD subtypes as a promising strategy for exploring ICI responders in GC. Metastatic pathways could be potential targets for GC patients with high immune infiltration but resistance to ICI therapy.
Learning with uncertainty to accelerate the discovery of histone lysine-specific demethylase 1A (KDM1A/LSD1) inhibitors
Authors: Wang Dong , Wu Zhenxing , Shen Chao , Bao Lingjie , Luo Hao , Wang Zhe , Yao Hucheng , Kong De-Xin , Luo Cheng , Hou Tingjun 
Published: December 2022

Abstract
Machine learning including modern deep learning models has been extensively used in drug design and screening. However, reliable prediction of molecular properties is still challenging when exploring out-of-domain regimes, even for deep neural networks. Therefore, it is important to understand the uncertainty of model predictions, especially when the predictions are used to guide further experiments. In this study, we explored the utility and effectiveness of evidential uncertainty in compound screening. The evidential Graphormer model was proposed for uncertainty-guided discovery of KDM1A/LSD1 inhibitors. The benchmarking results illustrated that (i) Graphormer exhibited comparative predictive power to state-of-the-art models, and (ii) evidential regression enabled well-ranked uncertainty estimates and calibrated predictions. Subsequently, we leveraged time-splitting on the curated KDM1A/LSD1 dataset to simulate out-of-distribution predictions. The retrospective virtual screening showed that the evidential uncertainties helped reduce false positives among the top-acquired compounds and thus enabled higher experimental validation rates. The trained model was then used to virtually screen an independent in-house compound set. The top 50 compounds ranked by two different ranking strategies were experimentally validated, respectively. In general, our study highlighted the importance to understand the uncertainty in prediction, which can be recognized as an interpretable dimension to model predictions.
Out of the Balkans and Anatolia to the Western Alps? Surprising phylogenetic implications for two endemicAlyssum(Brassicaceae) species:A. cognensesp. nov. andA. rossetii
Authors: Španiel Stanislav , Juillerat Philippe , Kaplan Klaus , Bovio Maurizio , Bäumler Beat , Perret Mathieu , Mártonfiová Lenka , Zozomová-Lihová Judita 
Published: December 2022

AbstractThe European Alps show a high degree of endemism associated mainly with the location of glacial refugia and environmental heterogeneity. Several Alpine endemics have evolved in the genus Alyssum. Here we study perennial Alyssum populations in the Western Alps, mainly distributed in the Aosta Valley region, which hosts high species diversity, although endemics are rare. We addressed the recently described stenoendemic A. rossetii and taxonomically uncertain populations usually attributed to A. montanum s.s. to clarify their phylogenetic position and morphological differentiation. The latter entity has been shown to be distinct from A. montanum s.s. and is described as a new species, Alyssum cognense, phylogenetically placed in the A. montanum–A. repens species complex. Both morphological and genetic patterns revealed that its closest relative occurs in the central Balkans. We present detailed ecological characteristics and morphological differentiation of A. cognense sp. nov. from its relatives and geographically closest species and speculate on its biogeographic origin. Genetic patterns (reduced diversity and nestedness) suggest long-distance dispersal from the central Balkan Peninsula. The second studied species, A. rossetii, is phylogenetically distant and belongs to the mainly Asian Alyssum section Gamosepalum lineage, which includes few representatives in southern and eastern Europe. The phylogenetically closest species of A. rossetii are Anatolian endemics, so this extreme disjunction remains puzzling. The present study illustrates the need for in-depth taxonomic and phylogenetic studies, even in well-explored Alpine regions, and also shows that the processes underlying the evolution of endemics can be complex and poorly understood.
Transcranial magnetic stimulation to the angular gyrus modulates the temporal dynamics of the hippocampus and entorhinal cortex
Authors: Coughlan Gillian , Bouffard Nichole R , Golestani Ali , Thakral Preston P , Schacter Daniel L , Grady Cheryl , Moscovitch Morris 
Published: December 2022

AbstractTranscranial magnetic stimulation (TMS) delivered to the angular gyrus (AG) affects hippocampal function and associated behaviors (Thakral PP, Madore KP, Kalinowski SE, Schacter DL. Modulation of hippocampal brain networks produces changes in episodic simulation and divergent thinking. 2020a. Proc Natl Acad Sci U S A. 117:12729–12740). Here, we examine if functional magnetic resonance imaging (fMRI)-guided TMS disrupts the gradient organization of temporal signal properties, known as the temporal organization, in the hippocampus (HPC) and entorhinal cortex (ERC). For each of 2 TMS sessions, TMS was applied to either a control site (vertex) or to a left AG target region (N = 18; 14 females). Behavioral measures were then administered, and resting-state scans were acquired. Temporal dynamics were measured by tracking change in the fMRI signal (i) “within” single voxels over time, termed single-voxel autocorrelation and (ii) “between” different voxels over time, termed intervoxel similarity. TMS reduced AG connectivity with the hippocampal target and induced more rapid shifting of activity in single voxels between successive time points, lowering the single-voxel autocorrelation, within the left anteromedial HPC and posteromedial ERC. Intervoxel similarity was only marginally affected by TMS. Our findings suggest that hippocampal-targeted TMS disrupts the functional properties of the target site along the anterior/posterior axis. Further studies should examine the consequences of altering the temporal dynamics of these medial temporal areas to the successful processing of episodic information under task demand.
Distinct neural activations correlate with maximization of reward magnitude versus frequency
Authors: Balasubramani Pragathi Priyadharsini , Diaz-Delgado Juan , Grennan Gillian , Alim Fahad , Zafar-Khan Mariam , Maric Vojislav , Ramanathan Dhakshin , Mishra Jyoti 
Published: December 2022

Abstract
Choice selection strategies and decision-making are typically investigated using multiple-choice gambling paradigms that require participants to maximize expected value of rewards. However, research shows that performance in such paradigms suffers from individual biases towards the frequency of gains such that users often choose smaller frequent gains over larger rarely occurring gains, also referred to as melioration. To understand the basis of this subjective tradeoff, we used a simple 2-choice reward task paradigm in 186 healthy human adult subjects sampled across the adult lifespan. Cortical source reconstruction of simultaneously recorded electroencephalography suggested distinct neural correlates for maximizing reward magnitude versus frequency. We found that activations in the parahippocampal and entorhinal areas, which are typically linked to memory function, specifically correlated with maximization of reward magnitude. In contrast, maximization of reward frequency was correlated with activations in the lateral orbitofrontal cortices and operculum, typical areas involved in reward processing. These findings reveal distinct neural processes serving reward frequency versus magnitude maximization that can have clinical translational utility to optimize decision-making.