bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying the geographic origins of invasiveMegathyrsus maximusin the United States using molecular data
Authors: Gaskin John F. , Goolsby John A. , Bon Marie-Claude , Cristofaro Massimo , Calatayud Paul-André
Published: May 2022

Megathyrsus maximusis nonnative in the neotropics, with a tall form that is commonly used as a forage grass and a smaller-statured form that is considered invasive in south Texas, USA. Biological control researchers are challenged to find an agent that will attack the short form, but not the desirable tall form in other parts of the neotropics. We conducted molecular analyses on 155Megathyrsus maximussamples from its native range in Africa and compared them with U.S. short-form samples to help determine the geographic origins of its invasion. We found eight distinct genotypes in 34 short-form samples from Texas and Florida, USA. The highest genetic similarity of invasive samples was with plants from South Africa, while highest matches for the desirable tall form were from Kenya, Uganda, Ivory Coast, and Zambia. Ongoing biological control agent exploration and research has found agents from Kenya that are associated with anM. maximusgenotype not well matched to the invasive short form, thus leading to a lack of rearing success. Two eriophyoid mite agents from the genetic match locality in South Africa have been evaluated but are not sufficiently host specific, as they develop on both the short and tall forms. Additional exploration is needed at the genetic match populations in South Africa to discover and evaluate potential biological control agents for the invasive form ofM. maximus.
Off-centre gravity induces large-scale flow patterns in spherical Rayleigh–Bénard convection
Authors: Wang Guiquan , Santelli Luca , Verzicco Roberto , Lohse Detlef , Stevens Richard J.A.M.
Published: May 2022

We perform direct numerical simulations to study the effect of the gravity centre offset in spherical Rayleigh–Bénard convection. When the gravity centre is shifted towards the south, we find that the shift of the gravity centre has a pronounced influence on the flow structures. At low Rayleigh number

$Ra$

, a steady-state large-scale meridional circulation induced by the baroclinic imbalance, created by the misalignment of the gravity potentials and isotherms, is formed. At high

$Ra$

, an energetic jet is created on the northern side of the inner sphere that is directed towards the outer sphere. The large-scale circulation induces a strong co-latitudinal dependence in the local heat flux. Nevertheless, the global heat flux is not affected by the changes in the large-scale flow organization induced by the gravity centre offset.
Crystal structure of merimepodib, C23H24N4O6
Authors: Kaduk James A. , Gates-Rector Stacy , Gindhart Amy M. , Blanton Thomas N.
Published: May 2022

The crystal structure of merimepodib has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Merimepodib crystallizes in space group P212121 (#19) with a = 4.60827(3), b = 12.30400(14), c = 37.9583(4) Å, V = 2152.241(20) Å3, and Z = 4. The crystal structure is dominated by two chains of N–H⋯O hydrogen bonds along the a-axis. The solid-state conformation has a similar general shape to the minimum-energy conformation, but different orientations of several of the rings. The differences indicate that intermolecular interactions are important in determining the solid-state conformation. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).
Breaking up data-enabled design: expanding and scaling up for the clinical context
Authors: Noortman Renee , Lovei Peter , Funk Mathias , Deckers Eva , Wensveen Stephan , Eggen Berry
Published: May 2022

Data-enabled design (DED) is a promising new methodology for designing with users from within their own context in an iterative and hands-on fashion. However, the agile and flexible qualities of the methodology do not directly translate to every context. In this article, we reflect on the design process of an intelligent ecosystem, called ORBIT, and a proposed evaluative study planned with it. This was part of a DED project in collaboration with a medical hospital to study the post-operative behavior in the (remote) context of bariatric patients. The design and preparation of this project and the process towards an eventual study rejection from the medical ethical committee (METC) provide rich insights into (1) what it means to conduct DED research in a clinical context, and (2) where the boundaries of the method might lie in this specific application area. We highlight insights from carefully designing the substantial infrastructure for the study, and how different aspects of DED translated less easily to the clinical context. We analyze the proposed study setup through the lenses of several modifications we made to DED and further reflect on how to expand and scale up the methodology and adapt the process for the clinical context.
Social isolation at the end of life: A case report of one person's journey navigating the medical landscape during the COVID-19 pandemic
Authors: Agosta Monica T. , Tang Michael , Carmack Cindy L. , Bruera Eduardo
Published: May 2022

Background

In addition to physical symptom burden, psychological suffering at end of life (EOL) is quite pervasive. As such, the interdisciplinary team in our Palliative and Supportive Care Unit strives to provide quality care sensitive to the physical and psychosocial needs of patients. Involving and allowing for the presence of family members is one way in which we afford our patients some additional comfort. Unfortunately, the current pandemic has placed limitations on this rather fundamental need for both patients and their family members. Here, we present a case illustrating the effects of visitor restrictions/isolation due to COVID-19 on the suffering of a patient at the EOL.

Case description

A male in his 20s with a refractory hematologic malignancy decided to pursue a comfort-based approach to care after a rapid clinical deterioration. Due to visitor restrictions, he had to face this decision with limited support at the bedside, which caused significant distress. He was forced to choose among several immediate family members who would be at his side through his hospitalization, to be his advocate, at times his voice, his confidant, and the person to relay all information to those on the outside. He expressed a wish to be married before he died, which occurred in our palliative care unit. This life goal was one we would normally encourage those he loved to gather around him, but this was not possible. He passed peacefully two days after he was married.

Conclusion

Although social limitations are necessary to help provide safety to the patients and staff in a hospital, they can have a direct impact on the suffering of patients and families at the EOL. Helping to maintain dignity, reflect on their life, and resolve any conflicts in the presence of family members is a benchmark for providing quality palliative care. Being barred from visitation due to isolation, threatens this care and lays the foundation for complicated grief among family members. Further research is needed to help balance the needs of those at the EOL with public safety. One such measure to help ease distress is to allow for more virtual visitation through electronic measures.
Disappearance of the Polar Cap Ionosphere During Geomagnetic Storm on 11 May 2019
Authors: Kwon H.‐J. , Kim K.‐H. , Jee G. , Seon J. , Lee C. , Ham Y.‐B. , Hong J. , Kim E. , Bullett T. , Auster H.‐U. , Magnes W. , Kraft S.
Published: May 2022

Multi‐instrument data from Jang Bogo Station (JBS) in Antarctica were utilized to study ionospheric responses to the 11 May 2019 moderate geomagnetic storm. These include Vertical Incident Pulsed Ionospheric Radar (VIPIR)/Dynasonde, Fabry‐Perot Interferometer (FPI), GPS vertical total electron content (vTEC), and magnetometer. The VIPIR/Dynasonde observed long‐lasting (>11 hr) severe depletion of the electron density in the F‐region ionosphere over JBS. During the depletion interval, GPS TEC also correspondingly decreased, FPI neutral temperature was significantly enhanced, and the polar magnetic field variations showed positive and negative excursions in the Y (east) and Z (vertical) components, respectively. GK‐2 A satellite, located ∼2.5 hr west of JBS, observed negative magnetic field perturbations in the azimuthal BD component at geosynchronous orbit during the depletion of ionospheric plasma. Such a BD perturbation at geosynchronous orbit is due to the field‐aligned currents flowing out of the ionosphere. From these observations we suggest that transpolar ionospheric currents connected to the field‐aligned currents flowing on a substorm wedge‐shaped circuit act as a source of polar atmospheric heating during the moderate geomagnetic storm interval and that elevated heavy molecular gases (O2 and N2) by atmospheric heating contribute to the electron density depletion via increased recombination rate.
Structural colour enhanced microfluidics
Authors: Qin Detao , Gibbons Andrew H. , Ito Masateru M. , Parimalam Sangamithirai Subramanian , Jiang Handong , Enis Karahan H. , Ghalei Behnam , Yamaguchi Daisuke , Pandian Ganesh N. , Sivaniah Easan
Published: May 2022

Advances in microfluidic technology towards flexibility, transparency, functionality, wearability, scale reduction or complexity enhancement are currently limited by choices in materials and assembly methods. Organized microfibrillation is a method for optically printing well-defined porosity into thin polymer films with ultrahigh resolution. Here we demonstrate this method to create self-enclosed microfluidic devices with a few simple steps, in a number of flexible and transparent formats. Structural colour, a property of organized microfibrillation, becomes an intrinsic feature of these microfluidic devices, enabling in-situ sensing capability. Since the system fluid dynamics are dependent on the internal pore size, capillary flow is shown to become characterized by structural colour, while independent of channel dimension, irrespective of whether devices are printed at the centimetre or micrometre scale. Moreover, the capability of generating and combining different internal porosities enables the OM microfluidics to be used for pore-size based applications, as demonstrated by separation of biomolecular mixtures.
Plant beta-diversity across biomes captured by imaging spectroscopy
Authors: Schweiger Anna K. , Laliberté Etienne
Published: May 2022

Monitoring the rapid and extensive changes in plant species distributions occurring worldwide requires large-scale, continuous and repeated biodiversity assessments. Imaging spectrometers are at the core of novel spaceborne sensor fleets designed for this task, but the degree to which they can capture plant species composition and diversity across ecosystems has yet to be determined. Here we use imaging spectroscopy and vegetation data collected by the National Ecological Observatory Network (NEON) to show that at the landscape level, spectral beta-diversity—calculated directly from spectral images—captures changes in plant species composition across all major biomes in the United States ranging from arctic tundra to tropical forests. At the local level, however, the relationship between spectral alpha- and plant alpha-diversity was positive only at sites with high canopy density and large plant-to-pixel size. Our study demonstrates that changes in plant species composition and diversity can be effectively and reliably assessed with imaging spectroscopy across terrestrial ecosystems at the beta-diversity scale—the spatial scale of spaceborne missions—paving the way for close-to-real-time biodiversity monitoring at the planetary level.
Simultaneous emulation of synaptic and intrinsic plasticity using a memristive synapse
Authors: Sung Sang Hyun , Kim Tae Jin , Shin Hyera , Im Tae Hong , Lee Keon Jae
Published: May 2022

Neuromorphic computing targets the hardware embodiment of neural network, and device implementation of individual neuron and synapse has attracted considerable attention. The emulation of synaptic plasticity has shown promising results after the advent of memristors. However, neuronal intrinsic plasticity, which involves in learning process through interactions with synaptic plasticity, has been rarely demonstrated. Synaptic and intrinsic plasticity occur concomitantly in learning process, suggesting the need of the simultaneous implementation. Here, we report a neurosynaptic device that mimics synaptic and intrinsic plasticity concomitantly in a single cell. Threshold switch and phase change memory are merged in threshold switch-phase change memory device. Neuronal intrinsic plasticity is demonstrated based on bottom threshold switch layer, which resembles the modulation of firing frequency in biological neuron. Synaptic plasticity is also introduced through the nonvolatile switching of top phase change layer. Intrinsic and synaptic plasticity are simultaneously emulated in a single cell to establish the positive feedback between them. A positive feedback learning loop which mimics the retraining process in biological system is implemented in threshold switch-phase change memory array for accelerated training.
Fast raster-scan optoacoustic mesoscopy enables assessment of human melanoma microvasculature in vivo
Authors: He Hailong , Schönmann Christine , Schwarz Mathias , Hindelang Benedikt , Berezhnoi Andrei , Steimle-Grauer Susanne Annette , Darsow Ulf , Aguirre Juan , Ntziachristos Vasilis
Published: May 2022

Melanoma is associated with angiogenesis and vascular changes that may extend through the entire skin depth. Three-dimensional imaging of vascular characteristics in skin lesions could therefore allow diagnostic insights not available by conventional visual inspection. Raster-scan optoacoustic mesoscopy (RSOM) images microvasculature through the entire skin depth with resolutions of tens of micrometers; however, current RSOM implementations are too slow to overcome the strong breathing motions on the upper torso where melanoma lesions commonly occur. To enable high-resolution imaging of melanoma vasculature in humans, we accelerate RSOM scanning using an illumination scheme that is coaxial with a high-sensitivity ultrasound detector path, yielding 15 s single-breath-hold scans that minimize motion artifacts. We apply this Fast RSOM to image 10 melanomas and 10 benign nevi in vivo, showing marked differences between malignant and benign lesions, supporting the possibility to use biomarkers extracted from RSOM imaging of vasculature for lesion characterization to improve diagnostics.
Cryo-EM structures define ubiquinone-10 binding to mitochondrial complex I and conformational transitions accompanying Q-site occupancy
Authors: Chung Injae , Wright John J. , Bridges Hannah R. , Ivanov Bozhidar S. , Biner Olivier , Pereira Caroline S. , Arantes Guilherme M. , Hirst Judy
Published: May 2022

Mitochondrial complex I is a central metabolic enzyme that uses the reducing potential of NADH to reduce ubiquinone-10 (Q10) and drive four protons across the inner mitochondrial membrane, powering oxidative phosphorylation. Although many complex I structures are now available, the mechanisms of Q10 reduction and energy transduction remain controversial. Here, we reconstitute mammalian complex I into phospholipid nanodiscs with exogenous Q10. Using cryo-EM, we reveal a Q10 molecule occupying the full length of the Q-binding site in the ‘active’ (ready-to-go) resting state together with a matching substrate-free structure, and apply molecular dynamics simulations to propose how the charge states of key residues influence the Q10 binding pose. By comparing ligand-bound and ligand-free forms of the ‘deactive’ resting state (that require reactivating to catalyse), we begin to define how substrate binding restructures the deactive Q-binding site, providing insights into its physiological and mechanistic relevance.
Optogenetic manipulation and photoacoustic imaging using a near-infrared transgenic mouse model
Authors: Kasatkina Ludmila A. , Ma Chenshuo , Matlashov Mikhail E. , Vu Tri , Li Mucong , Kaberniuk Andrii A. , Yao Junjie , Verkhusha Vladislav V.
Published: May 2022

Optogenetic manipulation and optical imaging in the near-infrared range allow non-invasive light-control and readout of cellular and organismal processes in deep tissues in vivo. Here, we exploit the advantages of Rhodopseudomonas palustris BphP1 bacterial phytochrome, which incorporates biliverdin chromophore and reversibly photoswitches between the ground (740–800 nm) and activated (620–680 nm) states, to generate a loxP-BphP1 transgenic mouse model. The mouse enables Cre-dependent temporal and spatial targeting of BphP1 expression in vivo. We validate the optogenetic performance of endogenous BphP1, which in the activated state binds its engineered protein partner QPAS1, to trigger gene transcription in primary cells and living mice. We demonstrate photoacoustic tomography of BphP1 expression in different organs, developing embryos, virus-infected tissues and regenerating livers, with the centimeter penetration depth. The transgenic mouse model provides opportunities for both near-infrared optogenetics and photoacoustic imaging in vivo and serves as a source of primary cells and tissues with genomically encoded BphP1.
Modelling the pyrenoid-based CO2-concentrating mechanism provides insights into its operating principles and a roadmap for its engineering into crops
Authors: Fei Chenyi , Wilson Alexandra T. , Mangan Niall M. , Wingreen Ned S. , Jonikas Martin C.
Published: May 2022

Many eukaryotic photosynthetic organisms enhance their carbon uptake by supplying concentrated CO2 to the CO2-fixing enzyme Rubisco in an organelle called the pyrenoid. Ongoing efforts seek to engineer this pyrenoid-based CO2-concentrating mechanism (PCCM) into crops to increase yields. Here we develop a computational model for a PCCM on the basis of the postulated mechanism in the green alga Chlamydomonas reinhardtii. Our model recapitulates all Chlamydomonas PCCM-deficient mutant phenotypes and yields general biophysical principles underlying the PCCM. We show that an effective and energetically efficient PCCM requires a physical barrier to reduce pyrenoid CO2 leakage, as well as proper enzyme localization to reduce futile cycling between CO2 and HCO3−. Importantly, our model demonstrates the feasibility of a purely passive CO2 uptake strategy at air-level CO2, while active HCO3− uptake proves advantageous at lower CO2 levels. We propose a four-step engineering path to increase the rate of CO2 fixation in the plant chloroplast up to threefold at a theoretical cost of only 1.3 ATP per CO2 fixed, thereby offering a framework to guide the engineering of a PCCM into land plants.
Neoantigen quality predicts immunoediting in survivors of pancreatic cancer
Authors: Łuksza Marta , Sethna Zachary M. , Rojas Luis A. , Lihm Jayon , Bravi Barbara , Elhanati Yuval , Soares Kevin , Amisaki Masataka , Dobrin Anton , Hoyos David , Guasp Pablo , Zebboudj Abderezak , Yu Rebecca , Chandra Adrienne Kaya , Waters Theresa , Odgerel Zagaa , Leung Joanne , Kappagantula Rajya , Makohon-Moore Alvin , Johns Amber , Gill Anthony , Gigoux Mathieu , Wolchok Jedd , Merghoub Taha , Sadelain Michel , Patterson Erin , Monasson Remi , Mora Thierry , Walczak Aleksandra M. , Cocco Simona , Iacobuzio-Donahue Christine , Greenbaum Benjamin D. , Balachandran Vinod P.
Published: May 2022

Cancer immunoediting1is a hallmark of cancer2that predicts that lymphocytes kill more immunogenic cancer cells to cause less immunogenic clones to dominate a population. Although proven in mice1,3, whether immunoediting occurs naturally in human cancers remains unclear. Here, to address this, we investigate how 70 human pancreatic cancers evolved over 10 years. We find that, despite having more time to accumulate mutations, rare long-term survivors of pancreatic cancer who have stronger T cell activity in primary tumours develop genetically less heterogeneous recurrent tumours with fewer immunogenic mutations (neoantigens). To quantify whether immunoediting underlies these observations, we infer that a neoantigen is immunogenic (high-quality) by two features—‘non-selfness’  based on neoantigen similarity to known antigens4,5, and ‘selfness’  based on the antigenic distance required for a neoantigen to differentially bind to the MHC or activate a T cell compared with its wild-type peptide. Using these features, we estimate cancer clone fitness as the aggregate cost of T cells recognizing high-quality neoantigens offset by gains from oncogenic mutations. With this model, we predict the clonal evolution of tumours to reveal that long-term survivors of pancreatic cancer develop recurrent tumours with fewer high-quality neoantigens. Thus, we submit evidence that that the human immune system naturally edits neoantigens. Furthermore, we present a model to predict how immune pressure induces cancer cell populations to evolve over time. More broadly, our results argue that the immune system fundamentally surveils host genetic changes to suppress cancer.
Deep Visual Proteomics defines single-cell identity and heterogeneity
Authors: Mund Andreas , Coscia Fabian , Kriston András , Hollandi Réka , Kovács Ferenc , Brunner Andreas-David , Migh Ede , Schweizer Lisa , Santos Alberto , Bzorek Michael , Naimy Soraya , Rahbek-Gjerdrum Lise Mette , Dyring-Andersen Beatrice , Bulkescher Jutta , Lukas Claudia , Eckert Mark Adam , Lengyel Ernst , Gnann Christian , Lundberg Emma , Horvath Peter , Mann Matthias
Published: May 2022

Despite the availabilty of imaging-based and mass-spectrometry-based methods for spatial proteomics, a key challenge remains connecting images with single-cell-resolution protein abundance measurements. Here, we introduce Deep Visual Proteomics (DVP), which combines artificial-intelligence-driven image analysis of cellular phenotypes with automated single-cell or single-nucleus laser microdissection and ultra-high-sensitivity mass spectrometry. DVP links protein abundance to complex cellular or subcellular phenotypes while preserving spatial context. By individually excising nuclei from cell culture, we classified distinct cell states with proteomic profiles defined by known and uncharacterized proteins. In an archived primary melanoma tissue, DVP identified spatially resolved proteome changes as normal melanocytes transition to fully invasive melanoma, revealing pathways that change in a spatial manner as cancer progresses, such as mRNA splicing dysregulation in metastatic vertical growth that coincides with reduced interferon signaling and antigen presentation. The ability of DVP to retain precise spatial proteomic information in the tissue context has implications for the molecular profiling of clinical samples.
Global gridded GDP data set consistent with the shared socioeconomic pathways
Authors: Wang Tingting , Sun Fubao
Published: May 2022

The vulnerability, exposure and resilience of socioeconomic activities to future climate extremes call for high-resolution gridded GDP in climate change adaptation and mitigation research. While global socioeconomic projections are provided mainly at the national level, and downscaling approaches using nighttime light (NTL) images or gridded population data can increase the uncertainty due to limitations. Therefore, we adopt an NTL-population-based approach, which exhibits higher accuracy in socioeconomic disaggregation. Gross regional product of over 800 provinces, which covering over 60% of the global land surface and accounted for more than 80% of GDP in 2005, were used as input. We present a first set of comparable spatially explicit global gridded GDP projections with fine spatial resolutions of 30 arc-seconds and 0.25 arc-degrees for the historical period of 2005 and for 2030–2100 at 10-year intervals under the five SSPs, accounting for the two-child policy in China. This gridded GDP projection dataset can broaden the applicability of GDP data, the availability of which is necessary for socioeconomic and climate change research.
Monitoring microseismicity of the Hengill Geothermal Field in Iceland
Authors: Grigoli Francesco , Clinton John F. , Diehl Tobias , Kaestli Philipp , Scarabello Luca , Agustsdottir Thorbjorg , Kristjansdottir Sigridur , Magnusson Rognvaldur , Bean Christopher J. , Broccardo Marco , Cesca Simone , Dahm Torsten , Hjorleifsdottir Vala , Cabrera Banu Mena , Milkereit Claus , Nooshiri Nima , Obermann Anne , Racine Roman , Rinaldi Antonio Pio , Ritz Vanille , Sanchez-Pastor Pilar , Wiemer Stefan
Published: May 2022

Induced seismicity is one of the main factors that reduces societal acceptance of deep geothermal energy exploitation activities, and felt earthquakes are the main reason for closure of geothermal projects. Implementing innovative tools for real-time monitoring and forecasting of induced seismicity was one of the aims of the recently completed COSEISMIQ project. Within this project, a temporary seismic network was deployed in the Hengill geothermal region in Iceland, the location of the nation’s two largest geothermal power plants. In this paper, we release raw continuous seismic waveforms and seismicity catalogues collected and prepared during this project. This dataset is particularly valuable since a very dense network was deployed in a seismically active region where thousand of earthquakes occur every year. For this reason, the collected dataset can be used across a broad range of research topics in seismology ranging from the development and testing of new data analysis methods to induced seismicity and seismotectonics studies.
Holistic health record for Hidradenitis suppurativa patients
Authors: Tricarico Paola Maura , Moltrasio Chiara , Gradišek Anton , Marzano Angelo V , Flacher Vincent , Boufenghour Wacym , von Stebut Esther , Schmuth Matthias , Jaschke Wolfram , Gams Matjaž , Boniotto Michele , Crovella Sergio
Published: May 2022

Hidradenitis suppurativa (HS) is a recurrent inflammatory skin disease with a complex etiopathogenesis whose treatment poses a challenge in the clinical practice. Here, we present a novel integrated pipeline produced by the European consortium BATMAN (Biomolecular Analysis for Tailored Medicine in Acne iNversa) aimed at investigating the molecular pathways involved in HS by developing new diagnosis algorithms and building cellular models to pave the way for personalized treatments. The objectives of our european Consortium are the following: (1) identify genetic variants and alterations in biological pathways associated with HS susceptibility, severity and response to treatment; (2) design in vitro two-dimensional epithelial cell and tri-dimensional skin models to unravel the HS molecular mechanisms; and (3) produce holistic health records HHR to complement medical observations by developing a smartphone application to monitor patients remotely. Dermatologists, geneticists, immunologists, molecular cell biologists, and computer science experts constitute the BATMAN consortium. Using a highly integrated approach, the BATMAN international team will identify novel biomarkers for HS diagnosis and generate new biological and technological tools to be used by the clinical community to assess HS severity, choose the most suitable therapy and follow the outcome.
Forecasting large-scale circulation regimes using deformable convolutional neural networks and global spatiotemporal climate data
Authors: Nielsen Andreas Holm , Iosifidis Alexandros , Karstoft Henrik
Published: May 2022

Classifying the state of the atmosphere into a finite number of large-scale circulation regimes is a popular way of investigating teleconnections, the predictability of severe weather events, and climate change. Here, we investigate a supervised machine learning approach based on deformable convolutional neural networks (deCNNs) and transfer learning to forecast the North Atlantic-European weather regimes during extended boreal winter for 1–15 days into the future. We apply state-of-the-art interpretation techniques from the machine learning literature to attribute particular regions of interest or potential teleconnections relevant for any given weather cluster prediction or regime transition. We demonstrate superior forecasting performance relative to several classical meteorological benchmarks, as well as logistic regression and random forests. Due to its wider field of view, we also observe deCNN achieving considerably better performance than regular convolutional neural networks at lead times beyond 5–6 days. Finally, we find transfer learning to be of paramount importance, similar to previous data-driven atmospheric forecasting studies.
Fusion of expert uncertain assessment in FMEA based on the negation of basic probability assignment and evidence distance
Authors: Yuan Yusong , Tang Yongchuan
Published: May 2022

Failure mode and effects analysis (FMEA) has been widely used for potential risk modeling and management. Expert evaluation is used to model the risk priority number to determine the risk level of different failure modes. Dempster–Shafer (D–S) evidence theory is an effective method for uncertain information modeling and has been adopted to address the uncertainty in FMEA. How to deal with conflicting evidence from different experts is an open issue. At the same time, different professional backgrounds of experts may lead to different weights in modeling the evaluation. How to model the relative weight of an expert is an important problem. We propose an improved risk analysis method based on triangular fuzzy numbers, the negation of basic probability assignment (BPA) and the evidence distance in the frame of D–S evidence theory. First, we summarize and organize the expert’s risk analysis results. Then, we model the expert’s assessments based on the triangular fuzzy numbers as BPAs and calculate the negation of BPAs. Third, we model the weight of expert based on the evidence distance in the evidence theory. Finally, the Murphy’s combination rule is used to fuse the risk assessment results of different experts and calculate the new risk priority number (RPN). At the end of this paper, we apply the proposed method to analyze seventeen failure modes of aircraft turbine blades. The experimental results verify the rationality and effectiveness of this method.
Mapping microbiome-redox spectrum and evaluating Microbial-Redox Index in chronic gastritis
Authors: Panigrahi Manas Kumar , Kaliaperumal Venkatesh , Akella Abhishek , Venugopal Giriprasad , Ramadass Balamurugan
Published: May 2022

Peptic ulcer disease (PUD) and chronic gastritis are prevalent in developing countries. The role of oxidative stress in the pathogenesis of gastrointestinal mucosal disorders is well recognized. In PUD, the gastric mucosa and its associated microbiome are subject to diet and stress-induced oxidative perturbations. Tissue redox potential (ORP) measurement can quantify oxidative stress, reflecting the balance between prooxidants and antioxidants. This study hypothesizes that the oxidative stress quantified by tissue ORP will be associated with characteristic changes in the mucosa-associated microbiome in PUD and gastritis. In addition, we propose using relative microbial abundance as a quantitative marker of mucosal health. Endoscopy was performed to obtain gastric mucosal biopsies from ten PUD and ten non-ulcer dyspepsia (NUD) patients. The tissue ORP was measured directly with a microelectrode using a biopsy specimen. A second specimen from an adjacent site was subjected to 16s rRNA gene sequencing. From the OTUs, the relative abundance of the microbial taxon in each of the samples was derived. We analyzed the genome of the predominant species for genes encoding the utilization of oxygen as an electron acceptor in respiration and for the presence of antioxidant defense mechanisms. The organisms were then grouped based on their established and inferred redox traits. Shannon diversity index and Species richness were calculated on rarefied data. The relative abundance of organisms that prefer high ORP over those that favor low ORP is conceived as the “Microbial Redox Index (MRI),” an indicator of mucosal health. In the gastric mucosa, aerobic species predominate and are more diverse than the anaerobes. The predominant aerobes are Helicobacter pylori and Sphingobacterium mizutaii. The abundance of these two species had an inverse correlation with the abundance of low ORP preferring anaerobes. Their relative abundance ratio (Microbial Redox Index) correlated with the tissue oxidation–reduction potential (ORP), a direct measure of oxidative stress. Correlation analysis also revealed that the abundance of all anaerobes inversely correlated with the dominant aerobic taxa. In addition, Shannon and Species richness diversity indices, the probable indicators of mucosal health, were negatively correlated with Microbial Redox Index. Using PUD as a prototype mucosal disease, this article describes a generalized approach to infer and quantify mucosal oxidative stress by analyzing the relative abundance of microorganisms that preferentially grow at the extremes of the tissue redox potential. This ratiometric Microbial Redox Index can also be assessed using simple qPCR without the need for sequencing. The approach described herein may be helpful as a widely applicable quantitative measure of mucosal health with prognostic and therapeutic implications.
Genome-wide identification of carbapenem-resistant Gram-negative bacterial (CR-GNB) isolates retrieved from hospitalized patients in Bihar, India
Authors: Kumari Namrata , Kumar Mukesh , Katiyar Amit , Kumar Abhay , Priya Pallavi , Kumar Bablu , Biswas Nihar Ranjan , Kaur Punit
Published: May 2022

Carbapenemase-producing clinical isolates are becoming more common over the world, posing a severe public health danger, particularly in developing nations like India. Carbapenem-resistant Gram-negative bacterial (CR-GNB) infection has become a fast-expanding global threat with limited antibiotic choice and significant mortality. This study aimed to highlight the carbapenem-resistance among clinical isolates of hospital admitted patients in Bihar, India. A cross-sectional study was conducted with 101 clinical isolates of Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa. All GNB isolates were tested for their antimicrobial susceptibility using Kirby-Bauer disc diffusion method. Double disc synergy test / modified Hodge test (DDST/MHT) were used to detect carbapenemase production by these isolates. Subsequently, these isolates were evaluated for carbapenem-resistance genes using whole-genome sequencing method. The overall percentage of carbapenem-resistance among GNB was (17/101) 16.8%. The genomic analysis of antimicrobial-resistance (AMR) demonstrates a significantly high prevalence of blaCTX-M followed by blaSHV, blaTEM, blaOXA, and blaNDM β-lactam or carbapenem resistance genes among clinical isolates of GNB. Co-occurrence of blaNDM with other beta-lactamase-encoding genes was found in 70.6% of carbapenemase-producing isolates. Our study highlights the mechanism of carbapenem-resistance to curb the overwhelming threat posed by the emergence of drug-resistance in India.
Age-period-cohort analysis of lung cancer mortality in China and Australia from 1990 to 2019
Authors: Wang Ning , Xu Zhiwei , Lui Chi-Wai , Wang Baohua , Hu Wenbiao , Wu Jing
Published: May 2022

Lung cancer (LC) is the leading cause of cancer death in China and Australia, the countries with different socioenvironmental contexts in the Western Pacific Region. Comparing the age-period-cohort effect on LC mortality (LCM) between the two countries can help plan interventions and draw lessons for countries in the region. We collected LCM estimates between 1990 and 2019 from the GBD 2019. Age-period-cohort modelling was applied to compute the net drift, local drift, cross-sectional age curve, longitudinal age curve, and the rate ratios (RRs) of period and cohort. China had a higher LC age-standardized mortality rate than Australia in 2019 (men: 58.10 [95% uncertainty interval (UI): 46.53, 70.89] vs. 30.13 [95% UI: 27.88, 32.31]/100,000 population; women: 22.86 [95% UI: 18.52, 27.52] vs. 17.80 [95% UI: 15.93, 19.34]/100,000 population). Period and cohort effects on LCM improved more markedly among Australian men (RR for period effect, from 1.47 [95% confidence interval (CI) 1.41, 1.53] to 0.79 [95% CI 0.75, 0.84]; RR for cohort effect, from 2.56 [95% CI 2.44, 2.68] to 0.36 [95% CI 0.11, 1.18]) and Chinese women (RR for period effect, from 1.06 [95% CI 1.01, 1.11] to 0.85 [95% CI 0.82, 0.89]; RR for cohort effect, from 0.71 [95% CI 0.65, 0.78] to 0.51 [95% CI 0.26, 1.03]) during the study period and birth cohort. The LCM in Chinese population aged 65 to 79 and Australian women aged 75 to 79 increased. Smoking and particulate matter (PM) contributed most to LCM in China, while smoking and occupational carcinogens contributed most in Australia. Decreasing period and cohort risks for LCM attributable to smoking and PM were more remarkable in Australia than in China. The LCM attributable to occupational carcinogens was higher in Australia than in China, particularly for those aged 60 to 79. Vigorous tobacco and PM control, which brought a substantial decline in LCM in Australia, may help reduce LCM in China. Australia should highlight LC prevention among people with occupational exposure. Chinese aged ≥ 65 and Australian women aged ≥ 75 should be the priorities for LC interventions.
Modeling pulsativity in the hypothalamic–pituitary–adrenal hormonal axis
Authors: Churilov Alexander N. , Milton John G.
Published: May 2022

A new mathematical model for biological rhythms in the hypothalamic–pituitary–adrenal (HPA) axis is proposed. This model takes the form of a system of impulsive time-delay differential equations which include pulsatile release of adrenocorticotropin (ACTH) by the pituitary gland and a time delay for the release of glucocorticoid hormones by the adrenal gland. Numerical simulations demonstrate that the model’s response to periodic and circadian inputs from the hypothalamus are consistent with those generated by recent models which do not include a pulsatile pituitary. In contrast the oscillatory phenomena generated by the impulsive delay equation mode occur even if the time delay is zero. The observation that the time delay merely introduces a small phase shift suggesting that the effects of the adrenal gland are “downstream” to the origin of pulsativity. In addition, the model accounts for the occurrence of ultradian oscillations in an isolated pituitary gland. These observations suggest that principles of pulse modulated control, familiar to control engineers, may have an increasing role to play in understanding the HPA axis.
Distinct clinicopathological and genomic features in solid and basaloid adenoid cystic carcinoma of the breast
Authors: Ji Juan , Zhang Fang , Duan Fanglei , Yang Hong , Hou Jun , Liu Yang , Dai Jie , Liao Qiong , Chen Xian , Liu Qingsong
Published: May 2022

Adenoid cystic carcinoma (AdCC) of the breast is a rare indolent carcinoma of salivary gland-type tumors, frequently associated with MYB genetic alteration. Solid and basaloid adenoid cystic carcinoma (SB-AdCC) is considered a sparse variant of AdCC. This study sought to search for clinicopathological and genomic features in SB-AdCC. Registered clinicopathological data on a cohort of 13 AdCC of the breast cases, including six conventional adenoid cystic carcinoma (C-AdCC) cases and seven SB-AdCC cases, were collected. MYB gene rearrangement via fluorescent in situ hybridization was investigated and MYB protein expression was evaluated by immunohistochemistry. Compared with C-AdCC, we found that the distribution of SB-AdCC cases were shifted to older age and were more frequently distant metastasis. Moreover, metastasis cases also showed a high (exceed 30%) Ki-67 index. Both groups showed MYB rearrangements and MYB protein expression, but they were less frequent in SB-AdCC than C-AdCC. To conclude, our results suggest that SB-AdCC is an aggressive variant of mammary AdCC with a higher incidence of distant metastases compared with C-AdCC, though they share common molecular features. A high Ki-67 index may be an adverse prognostic factor for metastasis.
Macromolecular crowding: how shape and interaction affect the structure, function, conformational dynamics and relative domain movement of a multi-domain protein
Authors: Das Nilimesh , Sen Pratik
Published: May 2022

We contemplate a systematic shape-dependent macromolecular crowding effect on various protein properties and possible correlations among them. It leads to some new insights into the mechanism of macromolecular crowding.
Cyanine dye-assembled composite upconversion nanoparticles for the sensing and cell imaging of nitrite based on a single particle imaging method
Authors: Liu Yunchun , Zhu Wanru , Wei Xinru , Wang Lun , Chen Hongqi
Published: May 2022

An upconversion luminescence total internal reflection single particle imaging method was developed for the sensing and cell imaging of nitrite.
Development of a novel peptide aptamer that interacts with the eIF4E capped-mRNA binding site using peptide epitope linker evolution (PELE)
Authors: Frosi Yuri , Ng Simon , Lin Yen-Chu , Jiang Shimin , Ramlan Siti Radhiah , Lama Dilraj , Verma Chandra S. , Asial Ignacio , Brown Christopher J.
Published: May 2022

Identifying new binding sites and poses that modify biological function are an important step towards drug discovery.
Anti-Stokes photoinduced electrochemiluminescence at a photocathode
Authors: Descamps Julie , Zhao Yiran , Yu Jing , Xu Guobao , Léger Yoan , Loget Gabriel , Sojic Neso
Published: May 2022

A novel light conversion scheme that combines a p-type semiconductor and a cathodic electrochemiluminescence system enables anti-Stokes conversion of incident photons.
Facile C–H bond activation on a transient gallium imide
Authors: Kassymbek Aishabibi , Spasyuk Denis , Dmitrienko Anton , Pilkington Melanie , Nikonov Georgii I.
Published: May 2022

In situimidation of the Ga(i) compound 1 by azide N3SiMe3results in transient monomeric imide NacNacGaNSiMe3amenable to C–H bond activation of a variety of substrates featuring hard donor sites.
Palladium-catalyzed Heck cyclization/carbonylation with formates: synthesis of azaindoline-3-acetates and furoazaindolines
Authors: Ye Hao , Wu Linhui , Zhang Minrui , Jiang Guomin , Dai Hong , Wu Xin-Xing
Published: May 2022

A palladium-catalyzed domino cyclization/carbonylation has been achieved to access all four isomers of the azaindoline family bearing ester functional groups and furoazaindoline derivatives.
The chaotropic effect of ions on the self-aggregating propensity of Whitlock's molecular tweezers
Authors: Devi Madhusmita , Paul Sandip
Published: May 2022

Effect of different aluminum salt solutions on Whitlock's molecular tweezers.
Improving the accuracy of the variational quantum eigensolver for molecular systems by the explicitly-correlated perturbative [2]R12-correction
Authors: Schleich Philipp , Kottmann Jakob S. , Aspuru-Guzik Alán
Published: May 2022

We provide an integration of an explicitly-correlated, perturbative correction into the variational quantum eigensolver, which is able to improve the energies of electronic systems and thus can reduce quantum resources needed for a certain accuracy.
Supraballs as spherical solid 3D superlattices of hydrophobic nanocrystals dispersed in water: nanoarchitectonics and properties
Authors: Pileni M. P.
Published: May 2022

Nanoheaters: FCC solid spherical nanocrystal assemblies either dispersed in solution or internalized in tumor cells.
Thermal expansion of free volume in “classic” and regulated dimethacrylates: photocured directly and via a mask to study pillar formation
Authors: Consolati Giovanni , Quasso Fiorenza , Yaynik Erkin , Briatico Vangosa Francesco , Šauša Ondrej , Ehrmann Katharina , Švajdlenková Helena
Published: May 2022

PALS and dilatometry applied to thermal expansion of cured dimethacrylates reveal cylindrical free volume holes expanding ‘anisotropically’ in a commonly used photopolymer (poly2M) and ‘isotropically’ in regulated dithiol-based resin (poly2M-co-EDDT).
Plasma-promoted reactions of the heterobimetallic anions CuNb− with dinitrogen and subsequent reactions with carbon dioxide: formation of C–N bonds
Authors: Chu Lan-Ye , Ding Yong-Qi , Wang Ming , Ma Jia-Bi
Published: May 2022

Plasma effect promotes the dissociation of NN bonds on the heterobimetallic anion CuNb−, leading to the formation of CuNbN2−. CuNbN2− further reacts with CO2 to obtain NCO−, therefore N2 and CO2 coupling reaction is realized at room temperature.
Challenges for optical nanothermometry in biological environments
Authors: Quintanilla Marta , Henriksen-Lacey Malou , Renero-Lecuna Carlos , Liz-Marzán Luis M.
Published: May 2022

Biological environments absorb and scatter light, which complicates the controlled illumination of internal thermal probes and distorts emitted light. To what extent is this a problem to measure temperature and how can it be faced?
Target and tissue selectivity of PROTAC degraders
Authors: Guenette Robert G. , Yang Seung Wook , Min Jaeki , Pei Baikang , Potts Patrick Ryan
Published: May 2022

In this review, we focus on recent progress towards making selective PROTAC molecules and new PROTAC technologies that will continue to push the boundaries of achieving target and tissue selectivity.
Gas-phase photoelectrocatalytic oxidation of volatile organic compounds using defective WO3/TiO2 nanotubes mesh
Authors: Wang Xiaoguang , Pan Honghui , Murugananthan Muthu , Sun Minghui , Zhang Yanrong
Published: May 2022

A ducted GPEC reactor equipped with defective WO3/TiO2 nanotube photoelectrodes was developed for VOC removal. Applying a tiny bias voltage promoted rapid carrier transfer and inhibited the recombination of carriers trapped by the bulk OVs.
Biomass-derived 2-methyltetrahydrofuran platform: a focus on precious and non-precious metal-based catalysts for the biorefinery
Authors: Alorku Kingdom , Shen Chen , Li Yuhang , Xu Ying , Wang Chenguang , Liu Qiying
Published: May 2022

The existing literature has been summarized and synthesized, providing a new outlook for the preparation of 2-methyltetrahydrofuran from biomass substrates using precious and non-precious metal catalysts.
Electrochemical cascade synthesis of α-thio-substituted masked aldehydes
Authors: Sharma Deepak , Hussain Yaseen , Sharma Manisha , Chauhan Pankaj
Published: May 2022

An unprecedented 3-component cascade synthesis of β,β-dialkoxy sulfides under mild electrochemical conditions has been achieved.
Engineered extracellular vesicles as intelligent nanosystems for next-generation nanomedicine
Authors: Fan Zhijin , Jiang Cheng , Wang Yichao , Wang Kaiyuan , Marsh Jade , Zhang Da , Chen Xin , Nie Liming
Published: May 2022

Engineered EVs containing an intelligent core have been designed to interact with a living host environment and function in an ideal situation. This review provides a new insight into design of next-generation EV-based theranostic platforms.
Impact of N-donor auxiliary ligands on two new Co(ii)-based MOFs with N-heterocyclic ligands and a magnetism study
Authors: Dong Xiuyan , Zhang Xiaoyu , Li Yuyan , Xiong Dingqi , Fu Pengkun , Afzal Mohd , Alarifi Abdullah , Sakiyama Hiroshi
Published: May 2022

These current results show that the use of Co(ii)-MOF chemistry, especially in the presence of various auxiliary linkers, is an efficient method to prepare multifunctional MOFs combining new outstanding structures and excellent properties.
Correction: Structure–property relationships of diketopyrrolopyrrole- and thienoacene-based A–D–A type hole transport materials for efficient perovskite solar cells
Authors: Kini Gururaj P. , Parashar Mritunjaya , Jahandar Muhammad , Lee Jaewon , Chung Sein , Cho Kilwon , Shukla Vivek Kumar , Singh Ranbir
Published: May 2022

Correction for ‘Structure–property relationships of diketopyrrolopyrrole- and thienoacene-based A–D–A type hole transport materials for efficient perovskite solar cells’ by Gururaj P. Kini et al., New J. Chem., 2022, DOI: https://doi.org/10.1039/d2nj00294a.