bluuebunny/crossref_metadata_2025 huggingface dataset:
The Use and Ethics of Digital Twins in Medicine
Authors: Iqbal Jeffrey David , Krauthammer Michael , Biller-Andorno Nikola
Published: November 2022

Digital Health Technologies (DHTs) are currently the subject of much debate both in terms of their technological frontiers as well as their ethical, legal and societal implications (ELSI). Regulation of such technologies as medical devices currently lacks behind their level of adoption. Digital Twins are the next evolution step of such DHTs and provide an opportunity to anticipate and act on ELSI before adoption again leaps before the necessary review. This paper introduces the concept and use cases of digital twins in medicine, then frames the debate through the lens of related technologies, machine learning and personalized medicine, and maps ethical challenges stemming from those. Finally, we lay out how digital twins may change and challenge the future practice of medicine.
A qualitative exploration of adolescents’ experiences of digital Dialectical Behaviour Therapy during the COVID-19 pandemic
Authors: Ramzan Natasha , Dixey Rebecca , Morris Andre
Published: November 2022

The UK government implemented national social-distancing measures in response to the global COVID19 pandemic. As a result, many appointments in the National Health Service (NHS) took place virtually, including psychological interventions in out-patient settings. This study explored the experiences of adolescents participating in a dialectical behaviour therapy (DBT-A) programme via teletherapy (i.e. via video or telephone call) in a Children and Adolescent Mental Health Service (CAMHS). Thirteen adolescents with emotion dysregulation and related problems completed an online qualitative survey about their experience and acceptance of DBT-A delivered virtually. Thematic analysis was conducted on the survey data and generated three over-arching themes: (1) sense of loss; (2) feeling uncontained; and (3) benefits of virtual DBT. These over-arching themes were composed of eight subthemes (‘loss of connection with group and therapist’; ‘loss of skills-building opportunities’; ‘limited privacy’; ‘lack of safe therapy space’; ‘difficult endings’; ‘home comforts’; ‘convenience and accessibility’; and ‘easier to participate with others’). This study suggests that adolescents doing virtual DBT-A need approaches that acknowledge and address the additional relational, emotional and practical challenges of online therapy while maintaining fidelity to the evidence-based treatment model. Suggestions for further research and preliminary practice guidelines are discussed.

Key learning aims

(1)

To learn about the experiences of adolescents participating in a DBT programme for adolescents (DBT-A) conducted virtually, including the challenges and benefits they identified.

(2)

To learn about implications for clinical practice and future research directions.
Metakognitionen und interozeptive Sensibilität bei der Wahrnehmung des Vorgefühls bei Tic-Störungen über die Lebensspanne
Authors: Schütteler Christina , Gerlach Alexander L.
Published: November 2022

Zusammenfassung. Fragestellung: Menschen mit Tic-Störungen (TS) berichten im Kindesalter selten, im Erwachsenenalter mehrheitlich von Vorgefühlen vor Ausführen eines Tics. Die Vorgefühle sind situationsabhängig und variieren sowohl intra- als auch interindividuell. Bei Jugendlichen wurden Zusammenhänge des Vorgefühls mit metakognitiven Überzeugungen gefunden, bei altersgemischten Stichproben Auffälligkeiten in interozeptiver Sensibilität. Wir untersuchten unter Berücksichtigung des Tic-Schweregrads den Zusammenhang von Vorgefühlen, Metakognitionen und interozeptiver Sensibilität über die Lebensspanne hinweg. Methodik: 59 TS-Betroffene nahmen an einer Online-Fragebogenstudie teil. Vorgefühle wurden über die Premonitory Urge for Tics Scale (PUTS) erfasst, der Tic-Schweregrad über den Selbstbeurteilungsbogen TIC (DISYPS-III: SBB-TIC), die interozeptive Bewusstheit über eine Kurzform der Bewusstheitsskala des Body Perception Questionnaire (BPQ-A) und metakognitive Überzeugungen in Bezug auf Tics über die Belief About Tics Scale (BATS). Ergebnisse: Erwachsene berichten höhere PUTS-Werte. Bei Kindern steigt die interozeptive Sensibilität mit zunehmendem Alter. Interozeptive Sensibilität korreliert mit der PUTS. BATS und BPQ sagen PUTS vorher, auch wenn für Tics und Alter kontrolliert wird. Schlussfolgerungen: Es ist davon auszugehen, dass die gefundenen altersabhängigen Entwicklungen des Vorgefühls im Jugendalter auf hirnphysiologische Reifungsprozesse zurückzuführen sind. Negative Metakognitionen und Interozeptionsfähigkeit sind jedoch ebenfalls von Bedeutung bei der Entstehung und Aufrechterhaltung von Vorgefühlen und könnten therapeutisch genutzt werden.
An Internal Waves Data Set From Sentinel‐1 Synthetic Aperture Radar Imagery and Preliminary Detection
Authors: Tao Mingkai , Xu Chengji , Guo Lingxi , Wang Xiaoqing , Xu Yanlang
Published: November 2022

Internal waves (IWs) are a widely occurring phenomenon in the global oceans. They have significant impacts on marine environments through their propagation mechanisms. In this study, we collect 390 satellite images with 775 labels from Sentinel‐1 Synthetic Aperture Radar (SAR) from 2014 to 2021 to construct a data set containing IW packets in Andaman Sea, South China Sea, Sulu Sea, and Celebes Sea, respectively. All the SAR images acquired are pre‐processed to provide clear IW packets for better visualization. To better detect IWs in global oceans automatically, a machine‐learning based model is proposed to focus on different channels and the spatial information. The precision, recall, and mean average precision of our improved model applied on the IW data set is up to 98.7%, 96.9%, and 98.9%, respectively. Various cases of IWs images are analyzed to illustrate detection quality in different stripes, scales, and propagation directions of IWs. The experimental results indicate that our data set is helpful to better detect IWs, and proposed network can accurately detect IWs in SAR images under various conditions.
Thermo‐Compositional Structure of the South American Platform Lithosphere: Evidence of Stability, Modification, and Erosion
Authors: Altoe Isabella , Goes Saskia , Assumpção Marcelo
Published: November 2022

Constraints on the structure of cratonic lithosphere are essential to improve our understanding of craton formation, evolution and long‐term stability. Here, we perform a joint inversion for the thermal and compositional structure of the mantle lithosphere below the South America Platform, using Rayleigh wave group velocities, elevation, and geoid height. Thick thermal lithosphere (200–300 km) is found below the southern Amazonian and São Francisco Cratons and adjoining Parecis and eastern Paraná Basins. The southern Rio de la Plata Craton also retains a 200–250 km thick keel. Compositionally, Amazonian, São Francisco, and Rio de la Plata lithosphere has a metasomatic and possibly eclogite signature similar to that of North American Proterozoic collision belts. Parecis and eastern Paraná lithosphere has likely been altered by Mesozoic plume activity throughout most of its depth, while the rest of the Paraná Basin and the Chaco and Pantanal Basins appear to have lost the lithospheric root below ∼100 km depth that was there during intracratonic basin formation. The low elevation and high geoid of the western Paraná Basin requires a dense (eclogite) layer within the crust/shallow lithosphere, possibly associated with the NeoProterozoic Western Paraná Suture Zone and/or Mesozoic plume activity, while topography and geoid of the basins further west and of the western Rio de la Plata craton seem affected by dynamic (subduction‐related) topography. Thus, the variable geophysical structure of the platform lithosphere reflects a history that involves besides some stable keels, significant modification and thinning.
Using Seafloor Geodesy to Detect Vertical Deformation at the Hikurangi Subduction Zone: Insights From Self‐Calibrating Pressure Sensors and Ocean General Circulation Models
Authors: Woods K. , Webb S. C. , Wallace L. M. , Ito Y. , Collins C. , Palmer N. , Hino R. , Savage M. K. , Saffer D. M. , Davis E. E. , Barker D. H. N.
Published: November 2022

Seafloor pressure sensor data is emerging as a promising approach to resolve vertical displacement of the seafloor in the offshore reaches of subduction zones, particularly in response to slow slip events (SSEs), although such signals are challenging to resolve due to sensor drift and oceanographic signals. Constraining offshore SSE slip distribution is of key importance to understanding earthquake and tsunami hazards posed by subduction zones. We processed seafloor pressure data from January to October 2019 acquired at the Hikurangi subduction zone, offshore New Zealand, to estimate vertical displacement associated with a large SSE that occurred beneath the seafloor array. The experiment included three self‐calibrating sensors designed to remove sensor drift, which, together with ocean general circulation models, were essential to the identification and correction of long‐period ocean variability remaining in the data after applying traditional processing techniques. We estimate that long‐period oceanographic signals that were not synchronous between pressure sensors and reference sites influenced our inferred displacements by 0.3–2.6 cm, suggesting that regionally deployed reference sites alone may not provide sufficient ocean noise correction. After incorporating long‐period ocean variability corrections into the processing, we calculate 1.0–3.3 cm of uplift during the SSE offshore Gisborne at northern Hikurangi, and 1.1–2.7 cm of uplift offshore the Hawke's Bay area at central Hikurangi. Some Hawke Bay displacements detected by pressure sensors near the trench were delayed by 6 weeks compared to the timing of slip onset detected by onshore Global Navigation Satellite System sites, suggesting updip migration of the SSE.
Mutant p53 in cancer: from molecular mechanism to therapeutic modulation
Authors: Chen Xiaohua , Zhang Taotao , Su Wei , Dou Zhihui , Zhao Dapeng , Jin Xiaodong , Lei Huiwen , Wang Jing , Xie Xiaodong , Cheng Bo , Li Qiang , Zhang Hong , Di Cuixia
Published: November 2022

TP53, a crucial tumor suppressor gene, is the most commonly mutated gene in human cancers. Aside from losing its tumor suppressor function, mutant p53 (mutp53) often acquires inherent, novel oncogenic functions, which is termed “gain-of-function”. Emerging evidence suggests that mutp53 is highly associated with advanced malignancies and poor prognosis, which makes it a target for development of novel cancer therapies. Herein, we provide a summary of our knowledge of the mutp53 types and mutp53 spectrum in cancers. The mechanisms of mutp53 accumulation and gain-of-function are also summarized. Furthermore, we discuss the gain-of-function of mutp53 in cancers: genetic instability, ferroptosis, microenvironment, and stemness. Importantly, the role of mutp53 in the clinic is also discussed, particularly with regard to chemotherapy and radiotherapy. Last, emphasis is given to emerging strategies on how to target mutp53 for tumor therapy. Thus, this review will contribute to better understanding of the significance of mutp53 as a target for therapeutic strategies.
Perovskite quantum dot-induced monochromatization for broadband photodetection of wafer-scale molybdenum disulfide
Authors: Kim Minji , Bae Garam , Kim Kyeong Nam , Jo Hyeong-ku , Song Da Som , Ji Seulgi , Jeon Dohyun , Ko Semin , Lee Seon Joo , Choi Sungho , Yim Soonmin , Song Wooseok , Myung Sung , Yoon Dae Ho , An Ki-Seok , Lee Sun Sook
Published: November 2022

Two-dimensional transition metal dichalcogenide (2D TMD) crystals are versatile platforms for realizing emergent optoelectronic devices. However, the ability to produce large-area 2D TMDs with spatial homogeneity and to accomplish broadband photodetection by tuning the operating wavelengths in photodetectors are two paramount prerequisites for practical applications of 2D TMD-based photodetectors. Here, we demonstrated all-solution-processed broadband photodetectors based on the wafer-scale perovskite quantum dots (PQDs)/MoS2 through light management via the monochromatization effect of the PQDs. The photodetectors exhibited broadband photodetection behavior that retained high photocurrents over a wide spectral range (254, 365, and 532 nm) by enhancing the photoresponse in the UV region through light management via the monochromatization effect of the PQDs. This intriguing strategy was proven with (i) electrical isolation realized by inserting an Al2O3 insulator between the PQDs and MoS2 and (ii) alteration of the PQD density. The rational nanohybrid-based photodetectors also exhibited superb air stability and exceptional bending durability.
Bowing-alleviated continuous bandgap engineering of wafer-scale WS2xSe2(1-x) monolayer alloys and their assembly into hetero-multilayers
Authors: Kang Hee Seong , Kang Jung Hoon , Lee Sol , Lee Kihyun , Koo Do Hyoung , Kim Yong-Sung , Hong Young Joon , Kim Yong-Jin , Kim Kwanpyo , Lee Donghun , Lee Chul-Ho
Published: November 2022

Bandgap engineering of compound semiconductors and the fabrication of bandgap-modulated heterostructures are important for enabling the development of modern optoelectronics. However, these engineering processes are challenging for two-dimensional (2D) semiconductors of transition metal dichalcogenides, particularly on a large scale. Herein, we report the wafer-scale homogeneous growth of composition-modulated WS2xSe2(1-x) alloys with a continuously tunable bandgap using metal–organic chemical vapor deposition. Well-optimized growth produces monolayer films with excellent homogeneity over the entire wafer. The substitutional atomic chalcogen (S, Se) concentration in WS2xSe2(1-x) alloys is precisely controlled by varying the flow rate of the metal–organic precursors, leading to a bandgap modulation from 1.67 to 2.05 eV, as determined from absorbance spectra. Notably, the optical bandgap of WS2xSe2(1-x) alloys exhibits a nearly linear relationship with the chalcogen composition, implying a low bowing effect. This bowing-alleviated bandgap modulation is attributed to the small lattice mismatch, strain relaxation, and thermodynamic miscibility in the WS2xSe2(1-x) alloys, as confirmed by density-functional theory calculations. Furthermore, the fabrication of hetero-multilayers by stacking differently alloyed films is demonstrated. The produced heterostructure film exhibits a broad spectral absorbance distinct from that of the individual layers. The findings of this study provide insights for the advancement of versatile design of functional 2D optoelectronics.
Sea-level rise will likely accelerate rock coast cliff retreat rates
Authors: Shadrick Jennifer R. , Rood Dylan H. , Hurst Martin D. , Piggott Matthew D. , Hebditch Bethany G. , Seal Alexander J. , Wilcken Klaus M.
Published: November 2022

Coastal response to anthropogenic climate change is of central importance to the infrastructure and inhabitants in these areas. Despite being globally ubiquitous, the stability of rock coasts has been largely neglected, and the expected acceleration of cliff erosion following sea-level rise has not been tested with empirical data, until now. We have optimised a coastal evolution model to topographic and cosmogenic radionuclide data to quantify cliff retreat rates for the past 8000 years and forecast rates for the next century. Here we show that rates of cliff retreat will increase by up to an order of magnitude by 2100 according to current predictions of sea-level rise: an increase much greater than previously predicted. This study challenges conventional coastal management practices by revealing that even historically stable rock coasts are highly sensitive to sea-level rise and should be included in future planning for global climate change response.
Prioritizing autoimmunity risk variants for functional analyses by fine-mapping mutations under natural selection
Authors: Pankratov Vasili , Yunusbaeva Milyausha , Ryakhovsky Sergei , Zarodniuk Maksym ,   Estonian Biobank Research Team, Metspalu Andres , Nelis Mari , Milani Lili , Mägi Reedik , Esko Tõnu , Yunusbayev Bayazit
Published: November 2022

Pathogen-driven selection shaped adaptive mutations in immunity genes, including those contributing to inflammatory disorders. Functional characterization of such adaptive variants can shed light on disease biology and past adaptations. This popular idea, however, was difficult to test due to challenges in pinpointing adaptive mutations in selection footprints. In this study, using a local-tree-based approach, we show that 28% of risk loci (153/535) in 21 inflammatory disorders bear footprints of moderate and weak selection, and part of them are population specific. Weak selection footprints allow partial fine-mapping, and we show that in 19% (29/153) of the risk loci under selection, candidate disease variants are hitchhikers, and only in 39% of cases they are likely selection targets. We predict function for a subset of these selected SNPs and highlight examples of antagonistic pleiotropy. We conclude by offering disease variants under selection that can be tested functionally using infectious agents and other stressors to decipher the poorly understood link between environmental stressors and genetic risk in inflammatory conditions.
Biological effects of the loss of homochirality in a multicellular organism
Authors: Banreti Agnes , Bhattacharya Shayon , Wien Frank , Matsuo Koichi , Réfrégiers Matthieu , Meinert Cornelia , Meierhenrich Uwe , Hudry Bruno , Thompson Damien , Noselli Stéphane
Published: November 2022

Homochirality is a fundamental feature of all known forms of life, maintaining biomolecules (amino-acids, proteins, sugars, nucleic acids) in one specific chiral form. While this condition is central to biology, the mechanisms by which the adverse accumulation of non-l-α-amino-acids in proteins lead to pathophysiological consequences remain poorly understood. To address how heterochirality build-up impacts organism’s health, we use chiral-selective in vivo assays to detect protein-bound non-l-α-amino acids (focusing on aspartate) and assess their functional significance in Drosophila. We find that altering the in vivo chiral balance creates a ‘heterochirality syndrome’ with impaired caspase activity, increased tumour formation, and premature death. Our work shows that preservation of homochirality is a key component of protein function that is essential to maintain homeostasis across the cell, tissue and organ level.
An atlas of amyloid aggregation: the impact of substitutions, insertions, deletions and truncations on amyloid beta fibril nucleation
Authors: Seuma Mireia , Lehner Ben , Bolognesi Benedetta
Published: November 2022

Multiplexed assays of variant effects (MAVEs) guide clinical variant interpretation and reveal disease mechanisms. To date, MAVEs have focussed on a single mutation type—amino acid (AA) substitutions—despite the diversity of coding variants that cause disease. Here we use Deep Indel Mutagenesis (DIM) to generate a comprehensive atlas of diverse variant effects for a disease protein, the amyloid beta (Aβ) peptide that aggregates in Alzheimer’s disease (AD) and is mutated in familial AD (fAD). The atlas identifies known fAD mutations and reveals that many variants beyond substitutions accelerate Aβ aggregation and are likely to be pathogenic. Truncations, substitutions, insertions, single- and internal multi-AA deletions differ in their propensity to enhance or impair aggregation, but likely pathogenic variants from all classes are highly enriched in the polar N-terminal region of Aβ. This comparative atlas highlights the importance of including diverse mutation types in MAVEs and provides important mechanistic insights into amyloid nucleation.
Accessing chiral sulfones bearing quaternary carbon stereocenters via photoinduced radical sulfur dioxide insertion and Truce–Smiles rearrangement
Authors: Huang Jiapian , Liu Fei , Zeng Ling-Hui , Li Shaoyu , Chen Zhiyuan , Wu Jie
Published: November 2022

From the viewpoint of synthetic accessibility and functional group compatibility, photoredox-catalyzed sulfur dioxide insertion strategy enables in situ generation of functionalized sulfonyl radicals from easily accessible starting materials under mild conditions, thereby conferring broader application potential. Here we present two complementary photoinduced sulfur dioxide insertion systems to trigger radical asymmetric Truce–Smiles rearrangements for preparing a variety of chiral sulfones that bear a quaternary carbon stereocenter. This protocol features broad substrate scope and excellent stereospecificity. Aside from scalability, the introduction of a quaternary carbon stereocenter at position β to bioactive molecule-derived sulfones further demonstrates the practicality and potential of this methodology.
A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome
Authors: Chitale Poonam , Lemenze Alexander D. , Fogarty Emily C. , Shah Avi , Grady Courtney , Odom-Mabey Aubrey R. , Johnson W. Evan , Yang Jason H. , Eren A. Murat , Brosch Roland , Kumar Pradeep , Alland David
Published: November 2022

H37Rv is the most widely usedMycobacterium tuberculosisstrain, and its genome is globally used as theM. tuberculosisreference sequence. Here, we present Bact-Builder, a pipeline that uses consensus building to generate complete and accurate bacterial genome sequences and apply it to three independently cultured and sequenced H37Rv aliquots of a single laboratory stock. Two of the 4,417,942 base-pair long H37Rv assemblies are 100% identical, with the third differing by a single nucleotide. Compared to the existing H37Rv reference, the new sequence contains ~6.4 kb additional base pairs, encoding ten new regions that include insertions in PE/PPE genes and new paralogs ofesxNandesxJ, which are differentially expressed compared to the reference genes. New sequencing and de novo assemblies with Bact-Builder confirm that all 10 regions, plus small additional polymorphisms, are also present in the commonly used H37Rv strains NR123, TMC102, and H37Rv1998. Thus, Bact-Builder shows promise as an improved method to perform accurate and reproducible de novo assemblies of bacterial genomes, and our work provides important updates to the primaryM. tuberculosisreference genome.
A Myb enhancer-guided analysis of basophil and mast cell differentiation
Authors: Matsumura Takayoshi , Totani Haruhito , Gunji Yoshitaka , Fukuda Masahiro , Yokomori Rui , Deng Jianwen , Rethnam Malini , Yang Chong , Tan Tze King , Karasawa Tadayoshi , Kario Kazuomi , Takahashi Masafumi , Osato Motomi , Sanda Takaomi , Suda Toshio
Published: November 2022

The transcription factor MYB is a crucial regulator of hematopoietic stem and progenitor cells. However, the nature of lineage-specific enhancer usage of the Myb gene is largely unknown. We identify the Myb −68 enhancer, a regulatory element which marks basophils and mast cells. Using the Myb −68 enhancer activity, we show a population of granulocyte-macrophage progenitors with higher potential to differentiate into basophils and mast cells. Single cell RNA-seq demonstrates the differentiation trajectory is continuous from progenitors to mature basophils in vivo, characterizes bone marrow cells with a gene signature of mast cells, and identifies LILRB4 as a surface marker of basophil maturation. Together, our study leads to a better understanding of how MYB expression is regulated in a lineage-associated manner, and also shows how a combination of lineage-related reporter mice and single-cell transcriptomics can overcome the rarity of target cells and enhance our understanding of gene expression programs that control cell differentiation in vivo.
An enantioselective four-component reaction via assembling two reaction intermediates
Authors: Yu Sifan , Chang Wenju , Hua Ruyu , Jie Xiaoting , Zhang Mengchu , Zhao Wenxuan , Chen Jinzhou , Zhang Dan , Qiu Huang , Liang Yong , Hu Wenhao
Published: November 2022

A reaction intermediate is a key molecular entity that has been used in explaining how starting materials converts into the final products in the reaction, and it is usually unstable, highly reactive, and short-lived. Extensive efforts have been devoted in identifying and characterizing such species via advanced physico-chemical analytical techniques. As an appealing alternative, trapping experiments are powerful tools in this field. This trapping strategy opens an opportunity to discover multicomponent reactions. In this work, we report various highly diastereoselective and enantioselective four-component reactions (containing alcohols, diazoesters, enamines/indoles and aldehydes) which involve the coupling of in situ generated intermediates (iminium and enol). The reaction conditions presented herein to produce over 100 examples of four-component reaction products proceed under mild reaction conditions and show high functional group tolerance to a broad range of substrates. Based on experimental and computational analyses, a plausible mechanism of this multicomponent reaction is proposed.
Accurate discharge and water level forecasting using ensemble learning with genetic algorithm and singular spectrum analysis-based denoising
Authors: Nguyen Anh Duy , Le Nguyen Phi , Vu Viet Hung , Pham Quoc Viet , Nguyen Viet Huy , Nguyen Minh Hieu , Nguyen Thanh Hung , Nguyen Kien
Published: November 2022

Forecasting discharge (Q) and water level (H) are essential factors in hydrological research and flood prediction. In recent years, deep learning has emerged as a viable technique for capturing the non-linear relationship of historical data to generate highly accurate prediction results. Despite the success in various domains, applying deep learning in Q and H prediction is hampered by three critical issues: a shortage of training data, the occurrence of noise in the collected data, and the difficulty in adjusting the model’s hyper-parameters. This work proposes a novel deep learning-based Q–H prediction model that overcomes all the shortcomings encountered by existing approaches. Specifically, to address data scarcity and increase prediction accuracy, we design an ensemble learning architecture that takes advantage of multiple deep learning techniques. Furthermore, we leverage the Singular-Spectrum Analysis (SSA) to remove noise and outliers from the original data. Besides, we exploit the Genetic Algorithm (GA) to propose a novel mechanism that can automatically determine the prediction model’s optimal hyper-parameters. We conducted extensive experiments on two datasets collected from Vietnam’s Red and Dakbla rivers. The results show that our proposed solution outperforms current techniques across a wide range of metrics, including NSE, MSE, MAE, and MAPE. Specifically, by exploiting the ensemble learning technique, we can improve the NSE by at least $$2\%$$

2
%

. Moreover, with the aid of the SSA-based data preprocessing technique, the NSE is further enhanced by more than $$5\%$$

5
%

. Finally, thanks to GA-based optimization, our proposed model increases the NSE by at least $$6\%$$

6
%

and up to $$40\%$$

40
%

in the best case.
Automated cell-type classification combining dilated convolutional neural networks with label-free acoustic sensing
Authors: Jeon Hyeon-Ju , Lim Hae Gyun , Shung K. Kirk , Lee O-Joun , Kim Min Gon
Published: November 2022

This study aimed to automatically classify live cells based on their cell type by analyzing the patterns of backscattered signals of cells with minimal effect on normal cell physiology and activity. Our previous studies have demonstrated that label-free acoustic sensing using high-frequency ultrasound at a high pulse repetition frequency (PRF) can capture and analyze a single object from a heterogeneous sample. However, eliminating possible errors in the manual setting and time-consuming processes when postprocessing integrated backscattering (IB) coefficients of backscattered signals is crucial. In this study, an automated cell-type classification system that combines a label-free acoustic sensing technique with deep learning-empowered artificial intelligence models is proposed. We applied an one-dimensional (1D) convolutional autoencoder to denoise the signals and conducted data augmentation based on Gaussian noise injection to enhance the robustness of the proposed classification system to noise. Subsequently, denoised backscattered signals were classified into specific cell types using convolutional neural network (CNN) models for three types of signal data representations, including 1D CNN models for waveform and frequency spectrum analysis and two-dimensional (2D) CNN models for spectrogram analysis. We evaluated the proposed system by classifying two types of cells (e.g., RBC and PNT1A) and two types of polystyrene microspheres by analyzing their backscattered signal patterns. We attempted to discover cell physical properties reflected on backscattered signals by controlling experimental variables, such as diameter and structure material. We further evaluated the effectiveness of the neural network models and efficacy of data representations by comparing their accuracy with that of baseline methods. Therefore, the proposed system can be used to classify reliably and precisely several cell types with different intrinsic physical properties for personalized cancer medicine development.
Climate suitability of the Mediterranean Basin for citrus black spot disease (Phyllosticta citricarpa) based on a generic infection model
Authors: Galvañ Anaïs , Boughalleb-M’Hamdi Naima , Benfradj Najwa , Mannai Sabrine , Lázaro Elena , Vicent Antonio
Published: November 2022

Citrus black spot (CBS), caused by the fungus Phyllosticta citricarpa, is associated with serious yield and quality losses. The climate suitability of the Mediterranean Basin for CBS development has been long debated. However, CBS has been described in Tunisia. In this study, a generic model was used to simulate potential infections by ascospores and pycnidiospores together with a degree-day model to predict the onset of ascospore release. High-resolution climatic data were retrieved from the ERA5-Land dataset for the citrus-growing regions in the Mediterranean Basin and other locations where CBS is present. In general, the onset of ascospore release was predicted to occur late in spring, but there is no agreement on the adequacy of this empirical model for extrapolation to the Mediterranean Basin. The generic model indicated that infections by ascospores and pycnidiospores would be concentrated mainly in autumn, as well as in spring for pycnidiospores. In contrast to previous studies, the percentage of hours suitable for infection was higher for pycnidiospores than for ascospores. The values obtained with the generic infection model for Tunisia and several CBS-affected locations worldwide were similar to those for other citrus-growing regions in Europe and Northern Africa. These results support previous work indicating that the climate of the Mediterranean Basin is suitable for CBS development.
Chemical composition, antibacterial efficacy, and antioxidant capacity of essential oil and oleoresin from Monodora myristica and Tetrapleura tetraptera in Southeast Nigeria
Authors: Okechukwu Queency N. , Ugwuona Fabian U. , Ofoedu Chigozie E. , Juchniewicz Szymon , Okpala Charles Odilichukwu R.
Published: November 2022

Specific to the West African sub-region, previous studies involving fruit, stem, and bark of Tetrapleura tetraptera as well as seeds of Monodora myristica have largely focused on phytochemical properties of aqueous and methanolic and ethanolic extracts. To supplement existing information, the chemical composition, antibacterial efficacy (tested against Escherichia coli and Staphylococcus aureus), and antioxidant capacity (1,1-diphenyl-2-picrylhydrazyl (DPPH∙) radical scavenging, ferric reducing power, and total antioxidant capacity) of essential oil and oleoresin extracted from T. tetraptera fruit and M. myristica seeds cultivated in Southeast Nigeria, were studied. Essential oil and oleoresin were respectively extracted by steam distillation and aqueous maceration. By way of gas chromatograph mass spectrometry (GC–MS) analysis, the chemical compounds from essential oil and oleoresin from M. myristica and T. Tetraptera samples totaled 6 and 5, as well as 27 and 16, respectively. Besides the oleoresin of M. myristica and the essential oil of T. tetraptera showing some resistance against S. aureus, the oleoresins seemed highly susceptible to E. coli—all of which demonstrated concentration-dependence to the antibacterial inhibition zone. Scavenging DPPH radical, reduction power activity, and total antioxidant capacity increased with essential oil and oleoresin extracts' concentrations, which positions M. myristica and T. tetraptera spices as very promising for food preservation, especially against autoxidation and microbial spoilage.
Effect of intake manifold geometry on cylinder-to-cylinder variation and tumble enhancement in gasoline direct injection engine
Authors: Shin Jisoo , Kim Donghwan , Son Yousang , Park Sungwook
Published: November 2022

In this study, the effect of intake manifold geometry on cylinder-to-cylinder variation was investigated considering the volumetric efficiency, early tumble development, turbulent kinetic energy, and spark plug gap velocity using computational fluid dynamic program, CONVERGE v2.4. The simulation model was validated based on the PIV experiment in the cylinder and Mie-scattering experiment of intake manifold, and its results agreed well with the experiment results. The curved intake manifold and straight manifold were compared. As a result, it was advantageous for cylinder-to-cylinder variation in the straight intake manifold compared to the curved intake manifold in perspective of volumetric efficiency which were a maximum deviation of 1.7% in curved manifold and 0.6% in straight manifold. And the straight manifold had an effect of the strengthening the in-cylinder flow, so that the turbulent kinetic energy near TDC was increased to maximum 11% than curved manifold. And considering the effect of manifold curve radius on in-cylinder flow intensity in straight manifold, with increasing engine speed, the in-cylinder flow intensified during compression with decreasing the intake manifold radius due to the short distance between manifold inlet and port. Especially at 2000 rpm, the tumble ratio increased 55% at intake manifold radius of 10 cm than of 7 cm at bTDC 280 deg. Therefore, for the purpose of enhancing the in-cylinder flow near spark plug timing, shortened distance between intake manifold inlet and port and increasing the manifold radius is required.
Fast-acting and injectable cryoneurolysis device
Authors: Moradi Tuchayi Sara , Wang Ying , Khodorova Alla , Pence Isaac J. , Stemmer-Rachamimov Anat , Evans Conor L. , Anderson R. Rox , Garibyan Lilit
Published: November 2022

Cryoneurolysis is an opioid-sparing therapy for long-lasting and reversible reduction of pain. We developed a nerve-selective method for cryoneurolysis by local injection of ice-slurry (− 5 to − 6 °C) that induced decrease in nocifensive response starting from about a week after treatment and lasting up to 8 weeks. In this study, we test the hypothesis that injection of colder slurry leads to faster onset of analgesia. Colder slurry (− 9ºC) was injected around the rat sciatic nerve to induce cryoneurolysis. Hematoxylin and Eosin (H&E) staining was used to examine histologic effects on surrounding tissues. Coherent anti-Stokes Raman scattering (CARS) microscopy was used to study effects on myelin sheaths. Functional tests were used to assess changes in sensory and motor function in the treated hind paw. No inflammation or scarring was detected in surrounding skin and muscle tissues at day 7 post slurry injection. Functional tests showed rapid onset reduction in mechanical pain sensitivity starting from day 1 and lasting up to day 98. CARS imaging demonstrated disintegration of myelin sheaths post treatment followed by complete recovery of nerve structure by day 140. In this study we showed that colder slurry (− 9 °C) produces more rapid onset and longer duration of analgesia, while remaining nerve-selective
Low-cost quasi-global optimization of expensive electromagnetic simulation models by inverse surrogates and response features
Authors: Koziel Slawomir , Pietrenko-Dabrowska Anna
Published: November 2022

Conceptual design of contemporary high-frequency structures is typically followed by a careful tuning of their parameters, predominantly the geometry ones. The process aims at improving the relevant performance figures, and may be quite expensive. The reason is that conventional design methods, e.g., based on analytical or equivalent network models, often only yield rough initial designs. This is especially the case for miniaturized components featuring considerable electromagnetic (EM) cross couplings, or antenna systems with non-negligible radiator coupling (e.g., MIMO, closely-spaced arrays). For reliability reasons, parametric optimization is carried out using EM simulation tools, which is a time-consuming task. In many cases, designer needs to resort to a global search, especially when handling several objectives and constraints is necessary, or the high-frequency structure under design is overly complex. Combination of both aforementioned factors makes it no longer possible to rely on engineering insight, even to detect a promising region of the design space. Unfortunately, nature-inspired algorithms, commonly employed for solving these tasks typically exhibit significant computational expenditures. This paper proposes a simple yet efficient method for globalized search using a response feature approach and inverse regression surrogates. Owing to less nonlinear dependence of the feature point coordinates on the system variables (as compared to the original responses, e.g.,S-parameter frequency characteristics), our methodology permits a rapid identification of the most appropriate regions of the parametric space, and further design tuning by means of local routines. At the same time, the overall optimization cost is comparable to the cost of local procedures. The proposed approach is validated using several high-frequency structures (a dual-band antenna, a microstrip coupler, an impedance matching transformer) optimized under different design scenarios. Global search capability and computational efficiency are demonstrated through comprehensive comparisons with multiple-start local search, as well as particle swarm optimizer, a representative nature-inspired algorithm.
Deep multiple instance learning for predicting chemotherapy response in non-small cell lung cancer using pretreatment CT images
Authors: Chang Runsheng , Qi Shouliang , Wu Yanan , Song Qiyuan , Yue Yong , Zhang Xiaoye , Guan Yubao , Qian Wei
Published: November 2022

The individual prognosis of chemotherapy is quite different in non-small cell lung cancer (NSCLC). There is an urgent need to precisely predict and assess the treatment response. To develop a deep multiple-instance learning (DMIL) based model for predicting chemotherapy response in NSCLC in pretreatment CT images. Two datasets of NSCLC patients treated with chemotherapy as the first-line treatment were collected from two hospitals. Dataset 1 (163 response and 138 nonresponse) was used to train, validate, and test the DMIL model and dataset 2 (22 response and 20 nonresponse) was used as the external validation cohort. Five backbone networks in the feature extraction module and three pooling methods were compared. The DMIL with a pre-trained VGG16 backbone and an attention mechanism pooling performed the best, with an accuracy of 0.883 and area under the curve (AUC) of 0.982 on Dataset 1. While using max pooling and convolutional pooling, the AUC was 0.958 and 0.931, respectively. In Dataset 2, the best DMIL model produced an accuracy of 0.833 and AUC of 0.940. Deep learning models based on the MIL can predict chemotherapy response in NSCLC using pretreatment CT images and the pre-trained VGG16 with attention mechanism pooling yielded better predictions.
Hypertensive disorders of pregnancy share common cfDNA methylation profiles
Authors: Spinelli Marialuigia , Zdanowicz Jarmila A. , Keller Irene , Nicholson Pamela , Raio Luigi , Amylidi-Mohr Sofia , Mosimann Beatrice , Surbek Daniel , Mueller Martin
Published: November 2022

Hypertensive disorders of pregnancy (HDP) contribute substantially to perinatal morbidity and mortality. Epigenetic changes point towards cardio-metabolic dysregulation for these vascular disorders. In early pregnancy, epigenetic changes using cell free DNA (cfDNA) are largely unexplored. We aimed to investigate these in HDP between 11 and 14 weeks of gestation by analysis of cfDNA methylation profiles in patients with hypertensive disorders. We identified patients without chronic hypertension but with subsequent development of preeclampsia (PE) (n = 11), with chronic hypertension (HT) but without PE development (n = 14), and lacking both PE and HT (n = 422). We matched patients according to PE risk factors into three groups (n = 5 each group): (1) PE: no HT but PE development, (2) HT: chronic hypertension but no PE and (3) Control: no PE or HT. We successfully optimized our cfDNA isolation process prior to whole genome bisulfite sequencing. Analysis of cfDNA methylation changes indicate a common predisposition in PE and HT groups, chiefly of maternal origin. Assessment of significant differentially methylated regions and annotated genes point towards a common cardiovascular predisposition in preeclampsia and hypertension groups in the first trimester. We postulate the pivotal role of the maternal cardiovascular system in HDP, which is already evident in the first trimester.
Stacked kinship CNN vs. GBLUP for genomic predictions of additive and complex continuous phenotypes
Authors: Nazzicari Nelson , Biscarini Filippo
Published: November 2022

Deep learning is impacting many fields of data science with often spectacular results. However, its application to whole-genome predictions in plant and animal science or in human biology has been rather limited, with mostly underwhelming results. While most works focus on exploring alternative network architectures, in this study we propose an innovative representation of marker genotype data and tested it against the GBLUP (Genomic BLUP) benchmark with linear and nonlinear phenotypes. From publicly available cattle SNP genotype data, different types of genomic kinship matrices are stacked together in a 3D pile from where 2D grayscale slices are extracted and fed to a deep convolutional neural network (DNN). We simulated nine phenotype scenarios with combinations of additivity, dominance and epistasis, and compared the DNN to GBLUP-A (computed using only the additive kinship matrix) and GBLUP-optim (additive, dominance, and epistasis kinship matrices, as needed). Results varied depending on the accuracy metric employed, with DNN performing better in terms of root mean squared error (1–12% lower than GBLUP-A; 1–9% lower than GBLUP-optim) but worse in terms of Pearson’s correlation (0.505 for DNN compared to 0.672 and 0.669 of GBLUP-A and GBLUP-optim for fully additive case; 0.274 for DNN, 0.279 for GBLUP-A, and 0.477 for GBLUP-optim for fully dominant case). The proposed approach offers a basis to explore further the application of DNN to tabular data in whole-genome predictions.
Gasification of Biomass: An Overview
Authors: Chauhan Garima , Sanchez Natalia Montoya , Halmenschlager Cibele Melo , Link Felix
Published: November 2022

Gasification of biomass for the production of renewable energy and chemicals has gained increasing attention in recent years. Although gasification is a mature technology for the conversion of coal, modifying the existing technology, as well as understanding the implications of the significant variation of biomass composition in the overall gasification process, is still a challenge. This chapter focuses on the process of biomass gasification to produce syngas, which can then be utilized in Fischer–Tropsch synthesis. Selection of feedstock, pretreatment, and the reaction chemistry of gasification are discussed to provide the basics of the gasification process. Details are provided of the practical applications of gasification, the reactor configuration used for gasification and the effect of various gasification parameters on the quality of syngas produced. This chapter also briefly covers current developments in the field of biomass gasification and possible operational challenges.
Sustainable Aviation Fuel from Biomass via Gasification and Fischer–Tropsch Synthesis
Authors: Dossow M. , Dieterich V. , Hanel A. , Fendt S.
Published: November 2022

The global growth in air traffic is expected to continue over the next few decades, and the most promising strategy to reduce greenhouse gas emissions from aviation is to use sustainable aviation fuel (SAF). The biomass-to-liquid (BtL) process is considered the most promising of several pathways for SAF production. In this process, syngas is converted into long-chain hydrocarbons via Fischer–Tropsch Synthesis (FTS). SAF produced via FTS is considered a drop-in fuel, which means that existing aircraft can be operated with SAF without any technical modifications, and the use of sustainable biomass residues shows high potential for emission reductions. In this chapter, the specific BtL-FT pathway used in the production of SAF consists of the torrefaction of lignocellulosic biomass, oxygen-blown entrained flow gasification, gas conditioning and FTS yielding liquid hydrocarbon fuels with a high selectivity toward SAF for further upgrading. Modeling of different path configurations – including material and heat integration, as well as process parameter variation – shows the potential of the BtL-FT pathway to efficiently produce SAF in both the short and medium term.
Biomass to Liquid Fuel via Fischer–Tropsch (BTL-FT) Synthesis: Process Description and Economic Analysis
Authors: Okoye-Chine Chike George , Gorimbo Joshua , Moyo Mahluli , Yao Yali , Liu Xinying , Hildebrandt Diane , Fox James Alistair
Published: November 2022

The technoeconomic assessment of the biomass-to-liquid process via Fischer–Tropsch synthesis (BTL-FT) has shown that large-scale BTL-FT production is not currently feasible because the estimated production costs of BTL-FT processes cannot yet compete with conventional fossil fuels. However, large-scale BTL-FT production may be feasible in the future with the introduction of subsidies, lower biomass prices, growth of biomass commodity markets, higher petroleum prices, and favorable, stricter climate legislation on transportation fuels. In addition, there is a need to develop more economical gasification technologies for the gasification of biomass into synthesis gas using product compositions that will meet Fischer–Tropsch (FT) synthesis requirements. Furthermore, a conscious effort has to be made to develop catalysts for FT synthesis with better activity and selectivity toward desired products and a low deactivation rate.