bluuebunny/crossref_metadata_2025 huggingface dataset:
Comprehensive single-cell sequencing reveals the stromal dynamics and tumor-specific characteristics in the microenvironment of nasopharyngeal carcinoma
Authors: Gong Lanqi , Kwong Dora Lai-Wan , Dai Wei , Wu Pingan , Li Shanshan , Yan Qian , Zhang Yu , Zhang Baifeng , Fang Xiaona , Liu Li , Luo Min , Liu Beilei , Chow Larry Ka-Yue , Chen Qingyun , Huang Jinlin , Lee Victor Ho-Fun , Lam Ka-On , Lo Anthony Wing-Ip , Chen Zhiwei , Wang Yan , Lee Anne Wing-Mui , Guan Xin-Yuan
Published: March 2021

The tumor microenvironment (TME) of nasopharyngeal carcinoma (NPC) harbors a heterogeneous and dynamic stromal population. A comprehensive understanding of this tumor-specific ecosystem is necessary to enhance cancer diagnosis, therapeutics, and prognosis. However, recent advances based on bulk RNA sequencing remain insufficient to construct an in-depth landscape of infiltrating stromal cells in NPC. Here we apply single-cell RNA sequencing to 66,627 cells from 14 patients, integrated with clonotype identification on T and B cells. We identify and characterize five major stromal clusters and 36 distinct subpopulations based on genetic profiling. By comparing with the infiltrating cells in the non-malignant microenvironment, we report highly representative features in the TME, including phenotypic abundance, genetic alternations, immune dynamics, clonal expansion, developmental trajectory, and molecular interactions that profoundly influence patient prognosis and therapeutic outcome. The key findings are further independently validated in two single-cell RNA sequencing cohorts and two bulk RNA-sequencing cohorts. In the present study, we reveal the correlation between NPC-specific characteristics and progression-free survival. Together, these data facilitate the understanding of the stromal landscape and immune dynamics in NPC patients and provides deeper insights into the development of prognostic biomarkers and therapeutic targets in the TME.
Acceleration of western Arctic sea ice loss linked to the Pacific North American pattern
Authors: Liu Zhongfang , Risi Camille , Codron Francis , He Xiaogang , Poulsen Christopher J. , Wei Zhongwang , Chen Dong , Li Sha , Bowen Gabriel J.
Published: March 2021

Recent rapid Arctic sea-ice reduction has been well documented in observations, reconstructions and model simulations. However, the rate of sea ice loss is highly variable in both time and space. The western Arctic has seen the fastest sea-ice decline, with substantial interannual and decadal variability, but the underlying mechanism remains unclear. Here we demonstrate, through both observations and model simulations, that the Pacific North American (PNA) pattern is an important driver of western Arctic sea-ice variability, accounting for more than 25% of the interannual variance. Our results suggest that the recent persistent positive PNA pattern has led to increased heat and moisture fluxes from local processes and from advection of North Pacific airmasses into the western Arctic. These changes have increased lower-tropospheric temperature, humidity and downwelling longwave radiation in the western Arctic, accelerating sea-ice decline. Our results indicate that the PNA pattern is important for projections of Arctic climate changes, and that greenhouse warming and the resultant persistent positive PNA trend is likely to increase Arctic sea-ice loss.
Structural resolution of switchable states of a de novo peptide assembly
Authors: Dawson William M. , Lang Eric J. M. , Rhys Guto G. , Shelley Kathryn L. , Williams Christopher , Brady R. Leo , Crump Matthew P. , Mulholland Adrian J. , Woolfson Derek N.
Published: March 2021

De novo protein design is advancing rapidly. However, most designs are for single states. Here we report a de novo designed peptide that forms multiple α-helical-bundle states that are accessible and interconvertible under the same conditions. Usually in such designs amphipathic α helices associate to form compact structures with consolidated hydrophobic cores. However, recent rational and computational designs have delivered open α-helical barrels with functionalisable cavities. By placing glycine judiciously in the helical interfaces of an α-helical barrel, we obtain both open and compact states in a single protein crystal. Molecular dynamics simulations indicate a free-energy landscape with multiple and interconverting states. Together, these findings suggest a frustrated system in which steric interactions that maintain the open barrel and the hydrophobic effect that drives complete collapse are traded-off. Indeed, addition of a hydrophobic co-solvent that can bind within the barrel affects the switch between the states both in silico and experimentally.
All-printed stretchable corneal sensor on soft contact lenses for noninvasive and painless ocular electrodiagnosis
Authors: Kim Kyunghun , Kim Ho Joong , Zhang Haozhe , Park Woohyun , Meyer Dawn , Kim Min Ku , Kim Bongjoong , Park Heun , Xu Baoxing , Kollbaum Pete , Boudouris Bryan W. , Lee Chi Hwan
Published: March 2021

Electroretinogram examinations serve as routine clinical procedures in ophthalmology for the diagnosis and management of many ocular diseases. However, the rigid form factor of current corneal sensors produces a mismatch with the soft, curvilinear, and exceptionally sensitive human cornea, which typically requires the use of topical anesthesia and a speculum for pain management and safety. Here we report a design of an all-printed stretchable corneal sensor built on commercially-available disposable soft contact lenses that can intimately and non-invasively interface with the corneal surface of human eyes. The corneal sensor is integrated with soft contact lenses via an electrochemical anchoring mechanism in a seamless manner that ensures its mechanical and chemical reliability. Thus, the resulting device enables the high-fidelity recording of full-field electroretinogram signals in human eyes without the need of topical anesthesia or a speculum. The device, superior to clinical standards in terms of signal quality and comfortability, is expected to address unmet clinical needs in the field of ocular electrodiagnosis.
Phylogenomic and biochemical analysis reassesses temperate marine yeast Yarrowia lipolytica NCIM 3590 to be Yarrowia bubula
Authors: Gaikwad Prashant , Joshi Swanand , Mandlecha Akshay , RaviKumar Ameeta
Published: March 2021

Yarrowia clade contains yeast species morphologically, ecologically, physiologically and genetically diverse in nature. Yarrowia lipolytica NCIM 3590 (NCIM 3590), a biotechnologically important strain, isolated from Scottish sea waters was reinvestigated for its phenotypic, biochemical, molecular and genomic properties as it exhibited characteristics unlike Y. lipolytica, namely, absence of extracellular lipolytic activity, growth at lower temperatures (less than 20 °C) and in high salt concentrations (10% NaCl). Molecular identification using ITS and D1/D2 sequences suggested NCIM 3590 to be 100% identical with reference strain Yarrowia bubula CBS 12934 rather than Y. lipolytica CBS 6124 (87% identity) while phylogenetic analysis revealed that it clustered with Y. bubula under a separate clade. Further, whole genome sequencing of NCIM 3590 was performed using Illumina NextSeq technology and the draft reported here. The overall genome relatedness values obtained by dDDH (94.1%), ANIb/ANIm (99.41/99.42%) and OrthoANI (99.47%) indicated proximity between NCIM 3590 and CBS 12934 as compared to the reference strain Y. lipolytica. No extracellular lipase activity could be detected in NCIM 3590 while LIP2 gene TBLASTN analysis suggests a low 42% identity with e value 2 e−77 and 62% coverage. Hence molecular, phylogenetic, genomics, biochemical and microbial analyses suggests it belongs to Yarrowia bubula.
Neoptile feathers contribute to outline concealment of precocial chicks
Authors: Rohr Veronika A. , Volkmer Tamara , Metzler Dirk , Küpper Clemens
Published: March 2021

Camouflage is a widespread strategy to increase survival. The cryptic plumage colouration of precocial chicks improves camouflage often through disruptive colouration. Here, we examine whether and how fringed neoptile feathers conceal the outline of chicks. We first conducted a digital experiment to test two potential mechanisms for outline concealment through appendages: (1) reduction of edge intensity and (2) luminance transition. Local Edge Intensity Analysis showed that appendages decreased edge intensity whereas a mean luminance comparison revealed that the appendages created an intermediate transition zone to conceal the object’s outline. For edge intensity, the outline diffusion was strongest for a vision system with low spatial acuity, which is characteristic of many mammalian chick predators. We then analysed photographs of young snowy plover (Charadrius nivosus) chicks to examine whether feathers increase outline concealment in a natural setting. Consistent with better camouflage, the outline of digitally cropped chicks with protruding feathers showed lower edge intensities than the outline of chicks without those feathers. However, the observed mean luminance changes did not indicate better concealment. Taken together, our results suggest that thin skin appendages such as neoptile feathers improve camouflage. As skin appendages are widespread, this mechanism may apply to many organisms.
Field evaluation of PGP Bacillus sp. strain D5 native to Crocus sativus, in traditional and non traditional areas, and mining of PGP genes from its genome
Authors: Magotra Shanu , Bhagat Nancy , Ambardar Sheetal , Ali Tahir , Hurek Barbara Reinhold , Hurek Thomas , Verma Praveen Kumar , Vakhlu Jyoti
Published: March 2021

Native Bacillus sp. strain D5 coded as (Bar D5) has been isolated from the saffron corm that showed plant growth promotion (PGP) properties and also inhibits the growth of corm rot causing Fusarium oxysporum R1 (Fox R1) in-vitro. Bar D5 was more efficient PGP bacterium in comparison to earlier reported native bio-formulations by our group. Pot assays and field evaluation of Bar D5 confirmed its in-vivo efficacy for PGP traits and biocontrol activity as well. Pot trials were followed by field trials at traditional (Kishtwar) and non-traditional (R.S Pura) saffron cultivation areas in Jammu and Kashmir. At both places, Bar D5 bio-formulation treatment led to the increase in root number & length, shoot number & length, flower number and number & weight of daughter corms. Additionally, it also decreased the corm rot disease incidence significantly. Priming of corms with bio-formulation resulted in the reduction of pathogenic fungal load by three fold at the depth of corm sowing from ground level. The shelf life/viability of Bar D5 based bio-formulation was found to be 52% (viable spores) for one year at room temperature. Draft genome sequence of Bar D5 revealed the presence of genes necessary for PGP and biocontrol activity. Further, confirmation of gene sequences and annotation was done by amplification, re-sequencing and mapping of PGP and biocontrol genes on draft genome. Bar D5 based bio-formulation can be provided to companies/researchers interested in saffron cultivation or bio-formulation production for commercial exploitation, since saffron is grown as revenue crop across continents. The present study bridges the gap between genomics and its field application.
A novel stepwise integrative analysis pipeline reveals distinct microbiota-host interactions and link to symptoms in irritable bowel syndrome
Authors: Polster Annikka , Öhman Lena , Tap Julien , Derrien Muriel , Le Nevé Boris , Sundin Johanna , Törnblom Hans , Cvijovic Marija , Simrén Magnus
Published: March 2021

Although incompletely understood, microbiota-host interactions are assumed to be altered in irritable bowel syndrome (IBS). We, therefore, aimed to develop a novel analysis pipeline tailored for the integrative analysis of microbiota-host interactions and association to symptoms and prove its utility in a pilot cohort. A multilayer stepwise integrative analysis pipeline was developed to visualize complex variable associations. Application of the pipeline was demonstrated on a dataset of IBS patients and healthy controls (HC), using the R software package to analyze colonic host mRNA and mucosal microbiota (16S rRNA gene sequencing), as well as gastrointestinal (GI) and psychological symptoms. In total, 42 IBS patients (57% female, mean age 33.6 (range 18–58)) and 20 HC (60% female, mean age 26.8 (range 23–41)) were included. Only in IBS patients, mRNA expression of Toll-like receptor 4 and genes associated with barrier function (PAR2, OCLN, TJP1) intercorrelated closely, suggesting potential functional relationships. This host genes-based “permeability cluster” was associated to mucosa-adjacent Chlamydiae and Lentisphaerae, and furthermore associated to satiety as well as to anxiety, depression and fatigue. In both IBS patients and HC, chromogranins, secretogranins and TLRs clustered together. In IBS patients, this host genes-based “immune-enteroendocrine cluster” was associated to specific members of Firmicutes, and to depression and fatigue, whereas in HC no significant association to microbiota was identified. We have developed a stepwise integrative analysis pipeline that allowed identification of unique host-microbiota intercorrelation patterns and association to symptoms in IBS patients. This analysis pipeline may aid in advancing the understanding of complex variable associations in health and disease.
A gene module identification algorithm and its applications to identify gene modules and key genes of hepatocellular carcinoma
Authors: Zhang Yan , Lin Zhengkui , Lin Xiaofeng , Zhang Xue , Zhao Qian , Sun Yeqing
Published: March 2021

To further improve the effect of gene modules identification, combining the Newman algorithm in community detection and K-means algorithm framework, a new method of gene module identification, GCNA-Kpca algorithm, was proposed. The core idea of the algorithm was to build a gene co-expression network (GCN) based on gene expression data firstly; Then the Newman algorithm was used to initially identify gene modules based on the topology of GCN, and the number of clusters and clustering centers were determined; Finally the number of clusters and clustering centers were input into the K-means algorithm framework, and the secondary clustering was performed based on the gene expression profile to obtain the final gene modules. The algorithm took into account the role of modularity in the clustering process, and could find the optimal membership module for each gene through multiple iterations. Experimental results showed that the algorithm proposed in this paper had the best performance in error rate, biological significance and CNN classification indicators (Precision, Recall and F-score). The gene module obtained by GCNA-Kpca was used for the task of key gene identification, and these key genes had the highest prognostic significance. Moreover, GCNA-Kpca algorithm was used to identify 10 key genes in hepatocellular carcinoma (HCC): CDC20, CCNB1, EIF4A3, H2AFX, NOP56, RFC4, NOP58, AURKA, PCNA, and FEN1. According to the validation, it was reasonable to speculate that these 10 key genes could be biomarkers for HCC. And NOP56 and NOP58 are key genes for HCC that we discovered for the first time.
Ablation of kynurenine 3-monooxygenase rescues plasma inflammatory cytokine levels in the R6/2 mouse model of Huntington’s disease
Authors: Bondulich Marie Katrin , Fan Yilan , Song Yeojin , Giorgini Flaviano , Bates Gillian P.
Published: March 2021

Kynurenine 3-monooxygenase (KMO) regulates the levels of neuroactive metabolites in the kynurenine pathway (KP), dysregulation of which is associated with Huntington’s disease (HD) pathogenesis. KMO inhibition leads to increased levels of neuroprotective relative to neurotoxic metabolites, and has been found to ameliorate disease-relevant phenotypes in several HD models. Here, we crossed KMO knockout mice to R6/2 HD mice to examine the effect of KMO depletion in the brain and periphery. KP genes were dysregulated in peripheral tissues from R6/2 mice and KMO ablation normalised levels of a subset of these. KP metabolites were also assessed, and KMO depletion led to increased levels of neuroprotective kynurenic acid in brain and periphery, and dramatically reduced neurotoxic 3-hydroxykunurenine levels in striatum and cortex. Notably, the increased levels of pro-inflammatory cytokines TNFa, IL1β, IL4 and IL6 found in R6/2 plasma were normalised upon KMO deletion. Despite these improvements in KP dysregulation and peripheral inflammation, KMO ablation had no effect upon several behavioural phenotypes. Therefore, although genetic inhibition of KMO in R6/2 mice modulates several metabolic and inflammatory parameters, these do not translate to improvements in primary disease indicators—observations which will likely be relevant for other interventions targeted at peripheral inflammation in HD.
Applicability of optical coherence tomography angiography (OCTA) imaging in Parkinson’s disease
Authors: Lauermann Jost L. , Sochurek Jan A. M. , Plöttner Pauline , Alten Florian , Kasten Meike , Prasuhn Jannik , Brüggemann Norbert , Ranjbar Mahdy
Published: March 2021

To evaluate the significance of motion artifacts in optical coherence tomography angiography (OCTA) images of patients with Parkinson’s disease (PD) and healthy controls. In this prospective, cross-sectional study subjects with medicated PD (ON) and healthy, age- and gender-matched volunteers were recruited. Participants underwent specific ophthalmological examinations, including OCTA. Angiograms of the superficial retinal capillary plexus were evaluated for the type and frequency of artifacts using a validated motion artifact score (MAS). A total of 30 PD patients (60 eyes), average disease duration of 9.61 ± 5.55 years, and 30 matched, healthy controls (60 eyes) were recruited. Twenty percent of all eyes had an eye disease, unknown to the participant, with a significant impact on OCTA results. After cleansing the dataset by excluding subjects with confounding ocular comorbidities 42 eyes of 28 PD patients and 53 eyes of 29 healthy controls were further evaluated. Overall MAS and all five subtypes of motion artifacts were comparable without significant differences between groups. OCTA can be used in treated PD patients (ON) without a significant increase in motion artifacts. Nevertheless, special attention should be paid to image quality during the acquisition of OCTA data, for which an experienced OCTA operator is useful.
Pictures of social interaction prompt a sustained increase of the smile expression and induce sociability
Authors: Mota Bruna Eugênia Ferreira , Rodrigues Paula Ohana , Lacerda Kíssyla Christine Duarte , David Isabel Antunes , Volchan Eliane , Campagnoli Rafaela Ramos , Souza Gabriela Guerra Leal
Published: March 2021

Viewing pictures of social interaction can facilitate approach behaviors. We conducted two studies to investigate if social interaction cues, empathy, and/or social touch modulate facial electromyographic (EMG) reactivity (as evidenced by the zygomaticus major and corrugator supercilii muscles) and mood states. We presented bonding pictures (depicting social interaction) and control pictures (without social interaction) while continuously recording zygomatic and corrugator EMG activities. In both studies, picture blocks were paired by valence and arousal. All participants were college students. In study 1, participants (n = 80, 47 women) read relevant priming texts immediately before viewing each block of 14 pictures. In study 2, participants did not read (n = 82, 63 women) priming texts before each block of 28 pictures. In study 1 and study 2, participants also completed mood states questionnaires to assess sociability and altruistic behavior. Empathy and social touch frequency were also assessed by self-reported questionnaires. In both studies, bonding pictures increased the zygomatic activity and the self-reported sociability feeling compared to control pictures. Only in study 2, bonding pictures decreased median corrugator activity compared to control pictures. We concluded that social interaction cues were efficient to increase sociability and prompt a sustained smile expression regardless of priming texts.
Potential of big data approach for remote sensing of vehicle exhaust emissions
Authors: Hao Lijun , Yin Hang , Wang Junfang , Wang Xiaohu , Ge Yunshan
Published: March 2021

At present, remote sensing (RS) is applied in detecting vehicle exhaust emissions, and usually the RS emission results in a definite vehicle specific power (VSP) range are used to evaluate vehicle emissions and identify high-emitting vehicles. When the VSP exceeds this range, the corresponding vehicle emission RS data will not be used to assess vehicle emissions. This method is equivalent to setting only one VSP Bin qualified for vehicle emission evaluation, and generally only one threshold limit is given for each emission pollutant without considering the fluctuation characteristics of vehicle emissions with VSP. Therefore, it is easy to cause misjudgment in identifying high-emitting vehicles and is not conducive to scientific management of vehicle emissions. In addition, the vehicle emissions outside the selected VSP Bin are more serious and should be included in the scope of supervision. This research proposed the methods of vehicle classifications and VSP Binning in order to categorize the driving conditions of each kind of vehicles, and a big data approach was proposed to analyze the vehicle emission RS data in each VSP Bin for vehicle emission evaluation.
Clinical and economic consequences of switching from omalizumab to mepolizumab in uncontrolled severe eosinophilic asthma
Authors: Carpagnano Giovanna Elisiana , Resta Emanuela , Povero Massimiliano , Pelaia Corrado , D’Amato Mariella , Crimi Nunzio , Scichilone Nicola , Scioscia Giulia , Resta Onofrio , Calabrese Cecilia , Pelaia Girolamo , Barbaro Maria Pia Foschino
Published: March 2021

Severe asthma is burdened by frequent exacerbations and use of oral corticosteroids (OCS), which worsen patients’ health and increase healthcare spending. The aim of this study was to assess the clinical and economic impact of switching from omalizumab (OMA) to mepolizumab (MEP) in patients eligible for both biologics, but not optimally controlled by omalizumab. We retrospectively enrolled uncontrolled severe asthmatic patients who switched from OMA to MEP during the last two years. Information included blood eosinophil count, asthma control test (ACT), spirometry, serum IgE, fractional exhaled nitric oxide (FeNO), OCS intake, drugs, exacerbations/hospitalizations, visits and diagnostic exams. Within the perspective of Italian National Health System, a pre- and post-MEP 12-month standardized total cost per patient was calculated. 33 patients were enrolled: five males, mean age 57 years, disease onset 24 years. At OMA discontinuation, 88% were OCS-dependent with annual mean rate of 4.0 clinically significant exacerbations, 0.30 exacerbations needing emergency room visits or hospitalization; absenteeism due to disease was 10.4 days per patient. Switch to MEP improved all clinical outcomes, reducing total exacerbation rate (RR = 0.06, 95% CI 0.03–0.14), OCS-dependent patients (OR = 0.02, 95% CI 0.005–0.08), and number of lost working days (Δ = − 7.9, 95% CI − 11.2 to − 4.6). Pulmonary function improved, serum IgE, FeNO and eosinophils decreased. Mean annual costs were €12,239 for OMA and €12,639 for MEP (Δ = €400, 95% CI − 1588–2389); the increment due to drug therapy (+ €1,581) was almost offset by savings regarding all other cost items (− €1,181). Patients with severe eosinophilic asthma, not controlled by OMA, experienced comprehensive benefits by switching to MEP with only slight increases in economic costs.
Verbal threat learning does not spare loved ones
Authors: Morato Cristina , Guerra Pedro , Bublatzky Florian
Published: March 2021

Significant others provide individuals with a sense of safety and security. However, the mechanisms that underlie attachment-induced safety are hardly understood. Recent research has shown beneficial effects when viewing pictures of the romantic partner, leading to reduced pain experience and defensive responding. Building upon this, we examined the inhibitory capacity of loved face pictures on fear learning in an instructed threat paradigm. Pictures of loved familiar or unknown individuals served as signals for either threat of electric shocks or safety, while a broad set of psychophysiological measures was recorded. We assumed that a long-term learning history of beneficial relations interferes with social threat learning. Nevertheless, results yielded a typical pattern of physiological defense activation towards threat cues, regardless of whether threat was signaled by an unknown or a loved face. These findings call into question the notion that pictures of loved individuals are shielded against becoming threat cues, with implications for attachment and trauma research.
Evaluation of CO2 emissions and energy use with different container terminal layouts
Authors: Budiyanto Muhammad Arif , Huzaifi Muhammad Hanzalah , Sirait Simon Juanda , Prayoga Putu Hangga Nan
Published: March 2021

Sustainable development of container terminals is based on energy efficiency and reduction in CO2 emissions. This study estimated the energy consumption and CO2 emissions in container terminals according to their layouts. Energy consumption was calculated based on utility data as well as fuel and electricity consumptions for each container-handling equipment in the container terminal. CO2 emissions were estimated using movement modality based on the number of movements of and distance travelled by each container-handling equipment. A case study involving two types of container terminal layouts i.e. parallel and perpendicular layouts, was conducted. The contributions of each container-handling equipment to the energy consumption and CO2 emissions were estimated and evaluated using statistical analysis. The results of the case study indicated that on the CO2 emissions in parallel and perpendicular layouts were relatively similar (within the range of 16–19 kg/TEUs). These results indicate that both parallel and perpendicular layouts are suitable for future ports based on sustainable development. The results can also be used for future planning of operating patterns and layout selection in container terminals.
Investigating the microbial ecology of coastal hotspots of marine nitrogen fixation in the western North Atlantic
Authors: Wang Seaver , Tang Weiyi , Delage Erwan , Gifford Scott , Whitby Hannah , González Aridane G. , Eveillard Damien , Planquette Hélène , Cassar Nicolas
Published: March 2021

Variation in the microbial cycling of nutrients and carbon in the ocean is an emergent property of complex planktonic communities. While recent findings have considerably expanded our understanding of the diversity and distribution of nitrogen (N2) fixing marine diazotrophs, knowledge gaps remain regarding ecological interactions between diazotrophs and other community members. Using quantitative 16S and 18S V4 rDNA amplicon sequencing, we surveyed eukaryotic and prokaryotic microbial communities from samples collected in August 2016 and 2017 across the Western North Atlantic. Leveraging and significantly expanding an earlier published 2015 molecular dataset, we examined microbial community structure and ecological co-occurrence relationships associated with intense hotspots of N2 fixation previously reported at sites off the Southern New England Shelf and Mid-Atlantic Bight. Overall, we observed a negative relationship between eukaryotic diversity and both N2 fixation and net community production (NCP). Maximum N2 fixation rates occurred at sites with high abundances of mixotrophic stramenopiles, notably Chrysophyceae. Network analysis revealed such stramenopiles to be keystone taxa alongside the haptophyte diazotroph host Braarudosphaera bigelowii and chlorophytes. Our findings highlight an intriguing relationship between marine stramenopiles and high N2 fixation coastal sites.
Comparative analysis of machine learning algorithms for computer-assisted reporting based on fully automated cross-lingual RadLex mappings
Authors: Maros Máté E. , Cho Chang Gyu , Junge Andreas G. , Kämpgen Benedikt , Saase Victor , Siegel Fabian , Trinkmann Frederik , Ganslandt Thomas , Groden Christoph , Wenz Holger
Published: March 2021

Computer-assisted reporting (CAR) tools were suggested to improve radiology report quality by context-sensitively recommending key imaging biomarkers. However, studies evaluating machine learning (ML) algorithms on cross-lingual ontological (RadLex) mappings for developing embedded CAR algorithms are lacking. Therefore, we compared ML algorithms developed on human expert-annotated features against those developed on fully automated cross-lingual (German to English) RadLex mappings using 206 CT reports of suspected stroke. Target label was whether the Alberta Stroke Programme Early CT Score (ASPECTS) should have been provided (yes/no:154/52). We focused on probabilistic outputs of ML-algorithms including tree-based methods, elastic net, support vector machines (SVMs) and fastText (linear classifier), which were evaluated in the same 5 × fivefold nested cross-validation framework. This allowed for model stacking and classifier rankings. Performance was evaluated using calibration metrics (AUC, brier score, log loss) and -plots. Contextual ML-based assistance recommending ASPECTS was feasible. SVMs showed the highest accuracies both on human-extracted- (87%) and RadLex features (findings:82.5%; impressions:85.4%). FastText achieved the highest accuracy (89.3%) and AUC (92%) on impressions. Boosted trees fitted on findings had the best calibration profile. Our approach provides guidance for choosing ML classifiers for CAR tools in fully automated and language-agnostic fashion using bag-of-RadLex terms on limited expert-labelled training data.
On the feasibility of hearing electrons in a 1D device through emitted phonons
Authors: Verma Amit , Nekovei Reza , Kauser Zahed
Published: March 2021

This work investigates the vibrational power that may potentially be delivered by electron-emitted phonons at the terminals of a device with a 1D material as the active channel. Electrons in a 1D material traversing a device excite phase-limited acoustic and optical phonon modes as they undergo streaming motion. At ultra-low temperature (4 K in this study, for example), in the near absence of background phonon activity, the emitted traveling phonons may potentially be collected at the terminals before they decay. Detecting those phonons is akin to hearing electrons within the device. Results here show that traveling acoustic phonons can deliver up to a fraction of a nW of vibrational power at the terminals, which is within the sensitivity range of modern instruments. The total vibrational power from traveling optical and acoustic phonons is found to be in order of nW. In this work, Ensemble Monte Carlo (EMC) simulations are used to model the behavior of a gate-all-around (GAA) field-effect transistor (FET), with a single-wall semiconducting carbon nanotube (SWCNT) as the active channel, and a free-hanging SWCNT between two contacts. Electronic band structure of the SWCNT is calculated within the framework of a tight-binding (TB) model. The principal scattering mechanisms are due to electron–phonon interactions using 1st order perturbation theory. A continuum model is used to determine the longitudinal acoustic (LA) and optical (LO) phonons, and a single lowest radial breathing mode (RBM) phonon is considered.
Author Correction: The development of a scoring and ranking strategy for a patient-tailored adverse drug reaction prediction in polypharmacy
Authors: Valeanu Andrei , Damian Cristian , Marineci Cristina Daniela , Negres Simona
Published: March 2021

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Highly sensitive MALDI-MS measurement of active ricin: insight from more potential deoxynucleobase-hybrid oligonucleotide substrates
Authors: Yang Jiewei , Wang Chenyu , Luo Li , Li Zhi , Xu Bin , Guo Lei , Xie Jianwei
Published: March 2021

One deoxynucleobase-hybrid oligonucleotide 12 (Rd12) substrate-containing functional Gd̲A̲GA loop was revealed as a substrate with more potential for the measurement of active ricin by MALDI-MS.
In silico design of additively manufacturable composite synthetic vascular conduits and grafts with tuneable compliance
Authors: Byrne Oisín , Coulter Fergal , Roche Ellen T. , O'Cearbhaill Eoin D.
Published: March 2021

In silico modelling can be a powerful design tool to predict the behaviour of additively manufacturable composite synthetic vascular conduits and grafts with tuneable compliance.
In situ manipulation of the d-band center in metals for catalytic activity in CO oxidation
Authors: Lee Kyung Rok , Yun Danim , Park Dae Sung , Yun Yang Sik , Song Chyan Kyung , Kim Younhwa , Park Jungwon , Yi Jongheop
Published: March 2021

The d-band center of metal is controlled by using in situ technique without the adding of other materials.
Quantitative determination of lithium depletion during rapid cycling in sulfide-based all-solid-state batteries
Authors: Shin Sung Soo , Kim Ji-Su , Choi Sungjun , Ji Ho-Il , Yoon Kyung Joong , Lee Jong-Ho , Chung Kyung Yoon , Kim Hyoungchul
Published: March 2021

Advanced techniques based on the distribution of relaxation times to quantify the complex interfacial resistances in all-solid-state batteries were applied.
Towards developing a criterion to characterize non-covalent bonds: a quantum mechanical study
Authors: Kumar Nandan , Saha Soumen , Sastry G. Narahari
Published: March 2021

Chemical bonds are central to chemistry, biology, and allied fields, but still, the criterion to characterize an interaction as a non-covalent bond has not been studied rigorously.
Exploration of irradiation intensity dependent external in-band quantum yield for ZnO and CuO/ZnO photocatalysts
Authors: Luo Kaiyi , Hu Wenyu , Wei Jiaxuan , Zhang Qiuping , Wu Zhonghao , Li Dongyang , Miao Feng , Huang Yi , Xu Min , Ma Jian , Li Chunhong , Chen Gang , Han Rui , Wang Xiaoyi , Cui Xudong , Ruterana Pierre
Published: March 2021

We developed an optical aperture based method to determine the relationship between external quantum yield and irradiative intensity, where intrinsic ZnO and CuO decorated ZnO could reach similar external quantum yields under strong light intensity.
Optimization of the drying process of autumn fruits rich in antioxidants: a study focusing on rosehip (Rosa canina L.) and sea buckthorn (Elaeagnus rhamnoides (L.) A. Nelson) and their bioactive properties
Authors: Moldovan Cadmiel , Babotă Mihai , Mocan Andrei , Menghini Luigi , Cesa Stefania , Gavan Alexandru , Sisea Cristian , Vodnar Dan C. , Dias Maria Inês , Pereira Carla , Ferreira Isabel C. F. R. , Crişan Gianina , Barros Lillian
Published: March 2021

The main goal of our work was to establish the optimal parameters for the drying process of rosehip and sea buckthorn fruits, in order to enhance the recovery of bioactive compounds from these vegetal matrices.
Plant-derived melatonin from food: a gift of nature
Authors: Cheng Guo , Ma Tingting , Deng Zhihao , Gutiérrez-Gamboa Gastón , Ge Qian , Xu Pingkang , Zhang Qianwen , Zhang Junxiang , Meng Jiangfei , Reiter Russel J. , Fang Yulin , Sun Xiangyu
Published: March 2021

The Chinese fairy tale of Shennong, the god of agriculture in China, who tasted hundreds of grasses to find foods and herbs for humans during the legend period.
Insights into the development of Cu-based photocathodes for carbon dioxide (CO2) conversion
Authors: Wang Keke , Ma Yanfang , Liu Yang , Qiu Weixin , Wang Qingmei , Yang Xuetao , Liu Min , Qiu Xiaoqing , Li Wenzhang , Li Jie
Published: March 2021

The development of Cu-based photocathodes plays a critical role in in the realm of PEC CO2reduction, especially for the formation of C2products.
A robust electrochemical immunosensor based on core–shell nanostructured silica-coated silver for cancer (carcinoembryonic-antigen-CEA) diagnosis
Authors: Singh Priyanka , Katkar Pranav K. , Patil Umakant M. , Bohara Raghvendra A.
Published: March 2021

The process flow of disposable electrochemical immunosensor fabrication.
Revisiting activity of some glucocorticoids as a potential inhibitor of SARS-CoV-2 main protease: theoretical study
Authors: Elmaaty Ayman Abo , Alnajjar Radwan , Hamed Mohammed I. A. , Khattab Muhammad , Khalifa Mohamed M. , Al-Karmalawy Ahmed A.
Published: March 2021

The global breakout of COVID-19 and raised death toll has prompted scientists to develop novel drugs capable of inhibiting SARS-CoV-2.
Waste to resource: preparation of an efficient adsorbent and its sustainable utilization in flame retardant polyurethane composites
Authors: Tu Bei , Zhou Keqing , Zhou Qianqian , Gong Kaili , Hu Dongtao
Published: March 2021

The main innovation of this work is to achieve resource recycling and environmental pollution control, and obtain flame retardant TPU composites with high added value simultaneously.
Accelerated AI development for autonomous materials synthesis in flow
Authors: Epps Robert W. , Volk Amanda A. , Reyes Kristofer G. , Abolhasani Milad
Published: March 2021

A surrogate model is designed to represent a microfluidic material synthesis system using 1000 automatically conducted experiments. With this model, over 600 000 experiments are simulated to optimize an AI-guided material synthesis algorithm.
Development of a bi-compound heterogeneous cocatalyst modified p-Si photocathode for boosting the photoelectrochemical water splitting performance
Authors: Chen Zhiwei , Li Yang , Wang Lin , Bu Yuyu , Ao Jin-Ping
Published: March 2021

Development of a novel bi-compound cocatalyst (MoS2/Rh–P) modified p-Si photocathode for boosting the photoelectrochemical water reduction performance.
Facile modulation of different vacancies in ZnS nanoplates for efficient solar fuel production
Authors: Li Pan , Guo Lingju , Chen Shuangming , Luo Gan , Zhu Shuang , Wang Yanjie , Song Li , He Tao
Published: March 2021

ZnS nanoplates with different types of defects are successfully prepared and accordingly exhibit different photocatalytic activity and selectivity for solar fuel production.
Combination of a large cation and coordinating additive improves carrier transport properties in quasi-2D perovskite solar cells
Authors: Sahayaraj Sylvester , Radicchi Eros , Ziółek Marcin , Ścigaj Mateusz , Tamulewicz-Szwajkowska Magdalena , Serafińczuk Jarosław , De Angelis Filippo , Wojciechowski Konrad
Published: March 2021

A Lewis base additive is used to stimulate vertical orientation and even the distribution of low dimensional perovskite crystallites, improving photovoltaic performance.
Revisiting the structural, electronic and photocatalytic properties of Ti and Zr based perovskites with meta-GGA functionals of DFT
Authors: Zulfiqar Waqas , Alay-e-Abbas Syed Muhammad , Abbas Ghulam , Laref Amel , Larsson J. Andreas , Shaukat Ali
Published: March 2021

Combining the SCAN and mBJ-LDA meta-GGA functionals of DFT facilitates accurate and efficient computation of physical properties of photocatalysts which is either comparable or better than computationally expansive hybrid functionals or GW methods.
Benzylic C–H addition of aromatic amines to alkenes using a scandium catalyst
Authors: Su Jianhong , Luo Yuncong , Xu Xin
Published: March 2021

Atom-economical and regioselective C(sp3)–C(sp3) bond formation has been achieved through benzylic C(sp3)–H alkylation of ortho-methyl anilines with alkenes using a scandium catalyst.
Radical-mediated alkoxypolyhaloalkylation of styrenes with polyhaloalkanes and alcohols via C(sp3)–H bond cleavage
Authors: Liang Yun-Yan , Huang Jing , Ouyang Xuan-Hui , Qin Jing-Hao , Song Ren-Jie , Li Jin-Heng
Published: March 2021

A radical-mediated alkoxypolyhaloalkylation of styrenes with polychloroalkanes and alcohols for the facile synthesis of complex polyhaloalkanes with excellent functional-group compatibility and a broad substrate scope.
Differentiating intramolecular spodium bonds from coordination bonds in two polynuclear zinc(ii) Schiff base complexes
Authors: Basak Tanmoy , Gomila Rosa M. , Frontera Antonio , Chattopadhyay Shouvik
Published: March 2021

Two new zinc(ii) complexes have been synthesized and characterized. Theoretical study is devoted to distinguish between conventional coordination bonds and spodium bonds between the zinc and oxygen centers.
Lifting the lid on the potentiostat: a beginner's guide to understanding electrochemical circuitry and practical operation
Authors: Colburn Alex W. , Levey Katherine J. , O'Hare Danny , Macpherson Julie V.
Published: March 2021

This article serves as an introductory tutorial to those with no formalised training in how an electrochemical potentiostat works. It highlights key electronic circuitry, signal conversion, noise, filters and provides practical trouble shooting tables.
Exploring the synergistic effect of B–N doped defective graphdiyne for N2 fixation
Authors: Cao Jingeng , Li Nan , Zeng Xin
Published: March 2021

The synergistic effect of B–N can effectively improve the catalytic activity of graphdiyne.
Probing supported bimetallic Pt–In sites in glycerol hydrogenolysis
Authors: do Valle Wanderson Ferraz , Soares André Von-Held , Xing Yutao , Passos Fabio Barboza
Published: March 2021

This work studied platinum and indium supported on alumina and silica as monometallic and bimetallic catalysts for the aqueous phase hydrogenolysis of glycerol towards 1,2-propanediol (1,2-PDO).
Gain and bandwidth of InP nanowire array photodetectors with embedded photogated InAsP quantum discs
Authors: Jeddi Hossein , Karimi Mohammad , Witzigmann Bernd , Zeng Xulu , Hrachowina Lukas , Borgström Magnus T. , Pettersson Håkan
Published: March 2021

We report on experimental results and advanced self-consistent simulations revealing a non-linear optical response, resulting from a trap-induced photogating mechanism, observed in InP nanowire array photoconductors with embedded InAsP quantum discs.
Interface engineering of cobalt–sulfide–selenium core–shell nanostructures as bifunctional electrocatalysts toward overall water splitting
Authors: Shi Zhengtian , Qi Xiangqian , Zhang Zhiyuan , Song Yingchao , Zhang Jianfa , Guo Chucai , Xu Wei , Liu Ken , Zhu Zhihong
Published: March 2021

We report for the first time that core–shell selenium cobalt disulfide nanotubes are successfully synthesized via a simple two-step method. The Se:CoS2−x electrode we obtained shows excellent electrocatalytic activity.
Biotin-decorated NIR-absorbing nanosheets for targeted photodynamic cancer therapy
Authors: Perumal Devanathan , Golla Murali , Pillai Kavya S. , Raj Gowtham , Krishna P. K. Anusree , Varghese Reji
Published: March 2021

Nanosheets derived from the self-assembly of the iodo-BODIPY–biotin conjugate as a photosensitizer for targeted PDT application is reported.
Metallaphotoredox catalysis with organic dyes
Authors: Gualandi Andrea , Anselmi Michele , Calogero Francesco , Potenti Simone , Bassan Elena , Ceroni Paola , Cozzi Pier Giorgio
Published: March 2021

Here…comes the fun…Combination of metals and organic photocatalysts allows the practical invention of new methodologies!
Biologically guided isolation and ADMET profile of new factor Xa inhibitors fromGlycyrrhiza glabraroots usingin vitroandin silicoapproaches
Authors: Ibrahim Reham S. , Mahrous Rahma S. R. , Abu EL-Khair Rasha M. , Ross Samir A. , Omar Abdallah A. , Fathy Hoda M.
Published: March 2021

Biologically guided isolation of new factor Xa inhibitors fromGlycyrrhiza glabraroots.
The effect of different thawing methods on the health-promoting compounds and antioxidant capacity in frozen baby mustard
Authors: Zhang Fen , Lin Pei-Xing , Xia Ping-Xin , Di Hong-Mei , Zhang Jia-Qi , Wang Zi-Han , Li Zhi-Qing , Huang Shu-Ya , Li Huan-Xiu , Sun Bo
Published: March 2021

The modifications in health-promoting compounds and antioxidant capacity of frozen baby mustard among the various thawing method were demonstrated.
Effect on thermal stability of microstructure and morphology of thermally-modified electrospun fibers of polybenzoxazines (PBz) blended with sulfur copolymers (SDIB)
Authors: Parreño Ronaldo P. , Liu Ying-Ling , Beltran Arnel B.
Published: March 2021

Microstucture and morphology of thermally-modified electrospun fiber of PBz blended with SDIB that enhanced structural satbility and integrity.
Monitoring the heme iron state in horseradish peroxidase to detect ultratrace amounts of hydrogen peroxide in alcohols
Authors: Ravanfar Raheleh , Abbaspourrad Alireza
Published: March 2021

Despite the importance of hydrogen peroxide (H2O2) in initiating oxidative damage and its connection to various diseases, the detection of low concentrations of H2O2 (<10 μM) is still limited using current methods, particularly in non-aqueous systems.
Removal of tetracycline hydrochloride from wastewater by Zr/Fe-MOFs/GO composites
Authors: Wei Fuhua , Ren Qinhui , Zhang Huan , Yang Lili , Chen Hongliang , Liang Zhao , Chen Ding
Published: March 2021

Zr/Fe-MOFs and Zr/Fe-MOFs/GO composites were prepared by solvothermal methods. They were characterized by SEM, FTIR, TGA and used for efficient removal of organic contaminants from aqueous solutions.
Porous shape-persistent rylene imine cages with tunable optoelectronic properties and delayed fluorescence
Authors: Huang Hsin-Hua , Song Kyung Seob , Prescimone Alessandro , Aster Alexander , Cohen Gabriel , Mannancherry Rajesh , Vauthey Eric , Coskun Ali , Šolomek Tomáš
Published: March 2021

Chiral rylene imine cages combine porosity and tunable optoelectronic properties. They adsorb CO2 over N2 with good selectivity and can show an efficient delayed fluorescence.
Inversing supramolecular chirality and boosting circularly polarized luminescence of pyrene moieties via a gel matrix
Authors: Bai Xue , Jiang Yuqian , Zhao Guangjiu , Jiang Jian , Yuan Chenhuan , Liu Minghua
Published: March 2021

Alkyl-substituted l/d-glutamide derivatives (L/D-SG) were designed as gelators to fabricate host gel matrices. Pyrene-appended l/d-glutamide derivatives (Py-LG/Py-DG) were employed as guest luminophores to investigate chiral packing and emission behavior in gel matrices.
Mining the key genes for ventilator-induced lung injury using co-expression network analysis
Authors: Li Zhao , Xiao Yajun , Xu Li , Wang Qingxiu
Published: March 2021

Mechanical ventilation is extensively adopted in general anesthesia and respiratory failure management, but it can also induce ventilator-induced lung injury (VILI). Therefore, it is of great urgency to explore the mechanisms involved in the VILI pathogenesis, which might contribute to its future prevention and treatment. Four microarray datasets from the GEO database were selected in our investigation, and were subjected to the Weighted Gene Co-Expression Network Analysis (WGCNA) to identify the VILI-correlated gene modules. The limma package in R software was used to identify the differentially expressed genes (DEGs) between the VILI and control groups. WGCNA was constructed by merging the GSE9314, GSE9368, GSE11434 and GSE11662 datasets. A total of 49 co-expression network modules were determined as associated with VILI. The intersected genes between hub genes screened from DEGs for VILI and those identified using WGCNA were as follows: Tlr2, Hmox1, Serpine1, Mmp9, Il6, Il1b, Ptgs2, Fos and Atf3, which were determined to be key genes for VILI. Those key genes were validated by GSE86229 and quantitative PCR (qPCR) experiment to have significantly statistical difference in their expression between the VILI and control groups. In a nutshell, nine key genes with expression differences in VILI were screened by WGCNA by integrating multiple datasets.