bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthesis of α-aryl sulfides by deaminative coupling of α-amino compounds with thiophenols
Authors: Yang Xuejing , Teng Qiang , Cao Feifei , Hu Jianfeng , Zhang Hao , Yang Yong
Published: April 2023

Amino substrates produce diazo compounds in situ and then form α-aryl sulfides by transition-metal-free deaminative coupling under mild conditions.
Preparation and compatibility mechanism study of the polyurethane-polysiloxane copolymer with tunable polysiloxane content for TPU/MVQ blends with comfortable texture
Authors: Lv Gege , Hu Jing , Hao Xinyue , Ning Nanying , Yu Bing , Tian Ming
Published: April 2023

The interface thickness of the TPU/MVQ blends can be adjusted by the PDMS content in the PU-PDMS copolymer compatibilizer, and the maximum interface thickness can be obtained with optimal PDMS content.
High-pressure behavior of hydrophobically coated gold nanoparticle supercrystals: role of the structure
Authors: Balédent Victor , Goldmann Claire , Ibrahim Helen , Pansu Brigitte
Published: April 2023

Mechanical properties of hydrophobically coated gold nanoparticle supercrystals have been studied by small angle X-ray scattering under quasi hydrostatic pressure for various nanoparticle core sizes, ligand length and supercrystal structure.
Highly controllable and reproducible one-step synthesis of β-NaYF4:Er3+@NaYbF4@NaYF4 upconversion nanoparticles for Sb2(S,Se)3 solar cells with enhanced efficiency
Authors: Jin Xin , Leow Shin Woei , Fang Yanan , Wong Lydia Helena
Published: April 2023

Monodisperse β-NaYF4:Er3+@NaYbF4@NaYF4 upconversion nanoparticles are synthesized using a one-step thermal decomposition process and further incorporated into the hole transporting layer to improve the efficiency of Sb2(S,Se)3 solar cells.
A high step‐up DC–DC converter with switched‐capacitor and switched‐inductor using one coupled inductor
Authors: Luo Peng , Liang Tsorng‐Juu , Chen Shih‐Ming , Chen Kai‐Hui
Published: April 2023

This paper proposes a high step‐up DC–DC converter which integrates switched‐inductor and switched‐capacitor techniques with a four‐winding coupled‐inductor. With switched‐inductor technique, two primary windings of the coupled‐inductor are charged in parallel and discharged in series to obtain high voltage gain. Moreover, by adding two sets of diode‐capacitor circuits on both primary side windings, not only can recycle the energy causing the voltage spike on the power switches, but can also lift the conversion ratio. Then, the power switches with lower voltage stress are used to improve the efficiency of the proposed converter. The operating principle, steady state analyses, and key parameters design of the proposed converter are discussed and provided. Finally, a 400 W laboratory prototype with 24 V input voltage and 480 V output voltage is constructed and tested to validate the performance. The highest and full load efficiencies are 95.8% and 94.8%, respectively.
Solar oxygen abundance using SST/CRISP center-to-limb observations of the O I 7772 Å line
Authors: Pietrow A. G. M. , Hoppe R. , Bergemann M. , Calvo F.
Published: April 2023

Solar oxygen abundance measurements based on the O Inear-infrared triplet have been a much debated subject for several decades, since non-local thermodynamic equilibrium (NLTE) calculations with 3D radiation-hydrodynamics model atmospheres introduced a large change to the 1D LTE modeling. In this work, we aim to test solar line formation across the solar disk using new observations obtained with the SST/CRISP instrument. The observed data set is based on a spectroscopic mosaic that stretches from disk center to the solar limb. By comparing the state-of-the-art 3D NLTE models with the data, we find that the 3D NLTE models provide an excellent description of the line formation across the disk. We obtain an abundance value ofA(O)=(8.73 ± 0.03) dex, with a very small angular dispersion across the disk. We conclude that spectroscopic mosaics are excellent probes for geometric and physical properties of hydrodynamics models and NLTE line formation.
15 Erfolgsfaktoren für schlanke Materiallogistik im OP
Authors: Roß Claudia , Lütte Katharina
Published: April 2023

Gerade die letzten Jahre zeigen, dass sich das allgemeine Sicherheitsgefühl der vergangenen Jahrzehnte auch in Krankenhäusern und deren Logistik ausgebreitet hatte und die plötzliche
Konfrontation mit Materialknappheit und gestiegenen Materialkosten diese Selbstverständlichkeit empfindlich störten. Für diese Punkte mussten kurzfristig kreative Lösungen gefunden und
langfristige Konzepte für die Zukunft geschaffen werden, die viele, bisher kaum denkbare Eventualitäten berücksichtigen
Stereoselective Total Synthesis of Stereoisomers of Entecavir
Authors: Wang Chao , Pei Dong , Zhou Li , Sun Jian
Published: April 2023

Practical methods for the synthesis of three stereoisomers of Entecavir have been developed. Starting from the reported intermediate (1S,2R)-2-((benzyloxy)methyl)cyclopent-3-en-1-ol and (1R,2S)-2-((benzyloxy)methyl)cyclopent-3-en-1-ol, respectively, three stereoisomers of Entecavir have been prepared with 17–20% overall yields. In principle, other stereoisomers could also be prepared by using the materials and reactions described in this article.
High quality colonoscopy: using textbook process as a composite quality measure
Authors: Nass Karlijn J. , van Doorn Sascha C. , Fockens Paul , Rees Colin J. , Pellisé Maria , van der Vlugt Manon , Dekker Evelien
Published: April 2023

Background High quality colonoscopy is fundamental to good patient outcomes. “Textbook outcome” has proven to be a feasible multidimensional measure for quality assurance between surgical centers. In this study, we sought to establish the “textbook process” (TP) as a new composite measure for the optimal colonoscopy process and assessed how frequently TP was attained in clinical practice and the variation in TP between endoscopists.

Methods To reach consensus on the definition of TP, international expert endoscopists completed a modified Delphi consensus process. The achievement of TP was then applied to clinical practice. Prospectively collected data in two endoscopy services were retrospectively evaluated. Data on colonoscopies performed for symptoms or surveillance between 1 January 2018 and 1 August 2021 were analyzed.

Results The Delphi consensus process was completed by 20 of 27 invited experts (74.1 %). TP was defined as a colonoscopy fulfilling the following items: explicit colonoscopy indication; successful cecal intubation; adequate bowel preparation; adequate withdrawal time; acceptable patient comfort score; provision of post-polypectomy surveillance recommendations in line with guidelines; and the absence of the use of reversal agents, early adverse events, readmission, and mortality. In the two endoscopy services studied, TP was achieved in 5962/8227 colonoscopies (72.5 %). Of 48 endoscopists performing colonoscopy, attainment of TP varied significantly, ranging per endoscopist from 41.0 % to 89.1 %.

Conclusion This study proposes a new composite measure for colonoscopy, namely “textbook process.” TP gives a comprehensive summary of performance and demonstrates significant variation between endoscopists, illustrating the potential benefit of TP as a measure in future quality assessment programs.
GAED Medal Lecture 2022: Challenging the Dogma in Diabetic Neuropathy and Beyond
Authors: Malik Rayaz A.
Published: April 2023

Dogma, according to the Britannica Dictionary, is ”a belief or set of beliefs that is accepted by the members of a group without being questioned or doubted.” Thus, in 2001, the heretical idea that corneal confocal microscopy (CCM)—an ophthalmic instrument—could be used to assess neurological disease truly challenged the dogma. The repurposing of CCM to study diabetic neuropathy and other neurodegenerative diseases is a wonderful illustration of being in the right time and place and having honest and open conversations between very different medical disciplines to 'challenge the dogma.' The Gulf Association of Diabetes and Endocrinology (GAED) Medal Lecture in 2022 and the European Association for the Study of Diabetes (EASD) Camillo Golgi Prize in 2019 have enabled me to tell my personal story in relation to the past, present, and future of CCM as a clinical tool to diagnose and predict neurodegeneration and identify nerve regeneration in clinical trials of new therapies for peripheral and central neurodegenerative diseases.
How bad is bad? Perceptual differences in the communication of severity in intimate partner violence
Authors: Sikström Sverker , Dahl Mats
Published: April 2023

Accurate communication of the severity of violence in intimate relations is essential for the appropriate evaluation of offenders and victims in contexts such as court trials, custody cases, and the continuation of relationships. Using a new paradigm, this study quantifies discrepancies in how the severity of violence is communicated in texts written by offenders, victims, and bystanders who witness violence. The study was conducted in two phases, where participants were randomly sampled from the same population to participate in either Phase 1 or Phase 2. In the first Phase, witnesses (narrators) provided nine narratives about self-experienced intimate partner violence and rated the violence’s severity; then in the second Phase non-witnesses (recipients) read all the narratives and rated the severity of the violence. Four types of perceptual differences (calibration, accuracy, gender, and role perceptual differences) were identified when rating the severity of three types of violence (psychological, physical, and sexual) as communicated by three types of witnesses (victims, offenders, and bystanders) of violence in heterosexual, romantic relationships. Several novel findings were made related to a strong perceptual difference in calibration, i.e., a tendency for the recipient to rate the violence more severely than the narrator, where this effect was mainly found for victims and bystanders, but not for offenders. Also, the calibration effect was largely seen in the sexual and physical, but not psychological, narratives. The recipients’ accuracy was considerably lower for psychological rather than sexual violence. Finally, the validity of the method was confirmed by replicating earlier findings on perceptual differences in roles where witnesses rated violence more severely than victims or offenders and women were rated more severely than men, which was especially true for male raters. These results suggest systematic perceptual differences in severity ratings and may have substantial implications for victims and offenders in real-life settings. These findings may potentially be used to ameliorate the negative effects of perceptual differences.
Historical record shows broad habitat use and rapid decline of the greater bilby Macrotis lagotis in eastern Australia
Authors: Silcock J. L. , McRae P. D. , Laidlaw M. J. , Southgate R. I.
Published: April 2023

Context Understanding historical distributions of species informs their ecology and response to threats, which can support management of surviving and translocated populations. Like many critical weight-range mammals in Australia, the greater bilby (Macrotis lagotis) has experienced major declines since European colonisation. The past distribution of bilbies in eastern Australia remains uncertain owing to the rapidity of their decline, their cryptic and nocturnal nature, and the paucity of specimen records. Aims We aimed to systematically collate, geo-reference and attribute bilby records from eastern Australia to better inform their historical distribution, habitat preferences, patterns of decline and response to threats. Methods We searched explorer and early settler journals, the digitised newspaper archive, interviews with long-term residents, Aboriginal language resources and ethnographies, place and property names, unpublished datasets, and documented locations of now-inactive bilby burrows. Records were geo-referenced and attributed with date, record type, source, location precision, bioregion, habitat and local abundance. The former distribution of bilby habitat in Queensland was modelled using Maxent, and the likely former occupancy of bilbies was identified using vegetation mapping. Key results More than 250 bilby records were found, only 34 of which appear in the Atlas of Living Australia. Sixty-five per cent of the records were attributed either ‘certain’ or ‘good’ reliability. Bilbies formerly occurred over most of inland New South Wales and the southern half of Queensland in areas receiving <600 mm average annual rainfall, in a wide variety of habitats. By the 1930s, bilbies were largely restricted to their current core range in south-western Queensland. This contraction in range coincided with the northward spread of rabbits and foxes. Conclusions Bilbies had a more contiguous distribution and occupied a wider range of habitats than was previously recognised. The species persisted in apparently isolated patches to the south-east, west and north of its present distribution until the 1970s, suggesting recent declines around the peripheries of its current range. By the 1990s, bilbies occupied <3% of their pre-1900 range in eastern Australia. Implications This work details changes in bilby distribution and provides key context for interpreting contemporary survey results. It also identifies areas where further surveys are required and may assist in selecting habitat for future translocations.
Phase jump detection and correction based on the support vector machine
Authors: Wang Y F , Hanada K , Sakurai D , Liu H Q , Lan T , Gao X , Wu X H
Published: April 2023

In general, interferometers are used to perform electron density measurements in magnetically confined plasma, where the electron density is dependent on the refractive index of the plasma. Measurements can be made through comparisons of the phase shift variation between the probe and reference laser beam. The plasma electron density should vary continuously during discharge; however, the fringe jump is a step-like change of the apparent electron density caused by a sudden jump of the measured phase shift. The appearance of fringe jump will degrade the interferometric measurements accuracy. This study attempted to solve the fringe jump problem on the polarimeter-interferometer (POINT) diagnostics system of the Experiment Advanced Superconducting Tokamak (EAST) by proposing a support vector machine model for electron density fringe jump detection and correction. The established model can efficiently classify the fringe jump data from the raw measurement data in a manner robust to noise and interference, and subsequently correct the jump. This model greatly improves the correction efficiency and precision of electron density data from the POINT system, and is expected to be embedded into the plasma control system to perform more accurate real-time electron density feedback control. Moreover, the algorithm is not limited to specific fusion devices or interferometer diagnostics, and is applicable to other interferometric measurement systems.
A window for cosmic strings
Authors: Auclair Pierre , Leyde Konstantin , A. Steer Danièle
Published: April 2023

Particle emission, in addition to gravitational radiation from cosmic string loops, affects the resulting loop distribution and hence the corresponding observational consequences of cosmic strings.
Here we focus on two models in which loops of length ℓ are produced from the infinite string network with a given power-law.
For both models we find that, due to particle production, the Stochastic Gravitational Wave Background (SGWB) is cut off outside the region of parameter space probed by any current or planned GW experiment.
Therefore the present constraints from the LIGO-Virgo-Kagra (LVK) collaboration still hold.
However for one of these models, if a fraction ≳𝒪(10-3) of these particles cascades into γ-rays, and if the gravitational backreaction scale follows the Polchinski-Rocha model, then the string tension is tightly constrained from below by measurements of the Diffuse γ-Ray Background, and from above by the SGWB.
With reasonable assumptions, the joint constraint on the string tension set by these two possible observables reduces the available parameter space of this cosmic string model to a narrow band. Future upgrades to LVK will either rule out this model or detect strings.
Gravitational waveform and polarization
from binary black hole inspiral in dynamical Chern-Simons gravity: from generation to propagation
Authors: Li Zhao , Qiao Jin , Liu Tan , Zhu Tao , Zhao Wen
Published: April 2023

We calculate the gravitational waveform radiated from spinning black holes (BHs) binary in
dynamical Chern-Simons (dCS) gravity. The equation of motion (EOM) of the spinning binary BHs is
derived based on the modified Mathisson-Papapetrou-Dixon equation for the spin-aligned circular
orbits. The leading-order effects induced by the dCS theory contain spin-spin interaction and
monopole-quadrupole interaction, which influences both the EOM of the binary system and
corresponding gravitational waveform at the second post-Newtonian (PN) order (i.e., 2PN
order). After reporting the waveforms, we investigate the polarization modes of gravitational
waves (GWs) in dCS theory. None of the extra modes appears in this theory up to the considered PN
order. Moreover, since the time scale of the binary merger is much smaller than that of the
cosmological expansion, the parity-violating effect of the dCS theory does not appear in the
process of GW generation. However, during the process of GW propagation, amplitude birefringence,
a typical parity-violating effect, makes plus and cross modes convert to each other, which
modifies the gravitational waveform at 1.5PN order.
Observation of electrostatic fluctuations driven by runaway electrons in EAST disruptions
Authors: Tang T. , Zeng L. , Qiu Z.Y. , Lin S.Y. , Sun Y.W. , Wei G.Y. , Zhu X. , Chen D.L. , Huang Y. , Duan Y.M. , Xu L.Q. , Zhuang H.D. , Liu H.Q. , Qian J.P , Luo C.X. , Ti A. , Zhao H.L. , Jie Y.X. , Liang Y.F. , Gao X.
Published: April 2023

Electrostatic fluctuations driven by runaway electrons (REs) have been observed following a thermal quench during Experimental Advanced Superconducting Tokamak–intended disruptions, which are triggered by massive gas injection. Electrostatic fluctuations are clearly detected using several radiation-related diagnostics and in two distinct frequency bands: 10–20 kHz and 30–40 kHz. The appearances of fluctuations are directly correlated with REs. Fluctuations observed during argon injection and neon injection have significantly different evolution with time, whereas no fluctuations can be found with helium injection. The measured frequency scales with different amounts of injected gases finally tend to be saturated. A clear phase difference is detected, and a mode structure of (m, n) = (1, 0) is identified in the soft x-ray detector array. Here, m and n are the poloidal and toroidal mode numbers, respectively. The geodesic acoustic mode proposed as a candidate instability is further discussed, and the barely trapped/passing electrons can contribute to drive the mode. Fluctuations are also correlated with significant RE loss, which supports the possibility of kinetic instability for RE mitigation in a tokamak reactor.
The use of Drone for Identifying and Mapping of Revegetation Plant in Coal Post-mines in Tanjung Enim, South Sumatra, Indonesia
Authors: Setyawan D , Hanum H , Warsito  , Achadi T , Paserena KD
Published: April 2023

Land reclamation and revegetation of post-mines need to be monitored regularly to ensure their progress. The drone is potential due to its high resolution and simplicity in operation and image processing. This study aimed to use the drone as an alternative in identifying and mapping land after the revegetation of coal post-mines in Tanjung Enim, South Sumatra, Indonesia. The research was conducted at the IUP Banko Barat of PT. Bukit Asam Co. Ltd, Indonesia. This research was conducted from September to December 2021. The method used in this study was a manual interpretation by making a delineation of the boundaries between types of revegetation plants in 2014, 2015, 2016, 2017, 2018, 2019, and 2020 planting years. The use of drones in this study was able to determine the distribution of revegetation plants used and produce the revegetation plant distribution map with 5 land cover classes, including Eucalyptus as the dominant species while Angsana (Pterocarpus indicus), Merbau (Intsia sp), Mahogany (Swietenia macrophylla), and Johar (Senna siamea) species with their patchy patterns, covering a total area of 22.52 ha or 66.44%. Eucalyptus is the most dominantly used as revegetation species in the coal post-mine in Tanjung Enim, with an area of 22.39 ha or 66.04% of the land. The drone is reliable for monitoring revegetation progress and may be used as a supplemental tool for evaluating post-mine conditions.
Investigation of 7075 aluminum alloy TIG welding joint using 7075 aluminum alloy wire before and after heat treatment
Authors: Xiao Liu , Chenyang Wang , Xiaoping Li , Bin Zhu , Runzhou Li
Published: April 2023

7075 aluminum alloy butt welding was carried out by TIG welding with self-made 7075 wire. The effects of different currents on the microstructure and mechanical properties of the joint before and after heat treatment were studied. Before heat treatment, the strength and elongation of the joint are 274.84 MPa and 6.3%, which are determined by the presence of a large number of second phase precipitates with different shapes. After heat treatment, the tensile strength and elongation are increased to 511.75 MPa and 13.76%. Since most of the second phase has been dissolved, the grain size becomes the decisive factor. The fine grain size and more sufficient recrystallization degree make the mechanical properties of the low-current joint better.
Comprehensive analysis of radiative cooling enabled thermoelectric energy harvesting
Authors: Zhu Yuxiao , Newbrook Daniel W , de Groot C H , Huang Ruomeng
Published: April 2023

The market for Internet-of-things (IoT) with integrated wireless sensor networks is expanding at a rate never seen before. The thriving of IoT also brings an unprecedented demand for sustainable micro-Watt-scale power supplies. Radiative cooling (RC) can provide a continuous temperature difference which can be converted by a thermoelectric generator (TEG) into electrical power. This novel combination of RC with TEG expands the category of sustainable energy sources for energy harvesting. However, the further application of RC-TEG requires a holistic investigation of its RC-TEG performance which is dependent on many different parameters. Using 3D finite element method simulation, this works provides a comprehensive analysis of the concept of RC-TEG by investigating the impact of radiative cooler properties, TEG parameters, and environmental conditions, to provide a full picture of the performance of RC-TEG devices. The capability of RC-TEG to provide continuous power supply is tested using real-time environmental data from both Singapore and London on two different days of the year, demonstrating continuous power supply sufficient for a wide range of physical devices.
Fault detection and classification in DC microgrid clusters
Authors: Pan Prateem , Mandal Rajib Kumar
Published: April 2023

With the rising popularity of DC microgrids, clusters of such grids are beginning to emerge as a practical and economical option. Short circuit problems in a DC microgrid clusters can cause overcurrent damage to power electronic devices. Protecting DC lines from large fault currents is essential. This paper presents a novel localized fault detection and classification technique for the protection of DC microgrid clusters. In this paper, a variational mode decomposition (VMD) and artificial neural network (ANN) based technique is proposed for accurate and effective fault detection and classification. This research aims to train an ANN that can detect and classify faults in DC microgrid clusters with multiple sources and loads by applying VMD to extract features of current signals. Different types of short circuit faults such as Pole to Pole and Pole to ground faults are considered under various grid operating conditions. The proposed method is capable of real-time fault detection and diagnosis, which can help prevent system failures and minimize downtime. The results indicate that the proposed approach is efficient and effective in detecting/classifying faults in DC microgrid clusters improving the reliability and system safety. The performance evaluation is carried out through rigorous case studies in MATLAB/Simulink environment to prove the efficacy of the proposed method. The VMD-ANN approach is shown to outperform other traditional signal processing techniques in terms of accuracy and robustness. Moreover, the proposed method is applicable to a wide range of DC microgrid clusters, making it a versatile and valuable tool for future research and development.
Optical detection of valley-polarized electron diffusion in diamond
Authors: Djurberg V , Majdi S , Suntornwipat N , Isberg J
Published: April 2023

Using the state of valley-polarization of electrons in solids is a promising new paradigm for information storage and processing. The central challenge in utilizing valley-polarization for this purpose is to develop methods for manipulating and reading out the final valley state. Here, we demonstrate optical detection of valley-polarized electrons in diamond. It is achieved by capturing images of electroluminescence from nitrogen-vacancy centers at the surface of a diamond sample that are excited by electrons drifting and diffusing through the sample. Monte Carlo simulations are performed to interpret the resulting experimental diffusion patterns. Our results give insight into the drift-diffusion of valley-polarized electrons in diamond and yield a way of analyzing the valley-polarization of ensembles of electrons.
Entire weak solutions for an anisotropic equation in the Heisenberg group
Authors: Razani Abdolrahman
Published: April 2023

Here, we consider an anisotropic equation
\[
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="minus normal upper Delta Subscript double-struck upper H Sub Superscript n Subscript comma ModifyingAbove p With right-arrow Baseline u plus a left-parenthesis q right-parenthesis StartAbsoluteValue u EndAbsoluteValue Superscript p Super Superscript en-dash Superscript 2 Baseline u equals lamda w left-parenthesis q right-parenthesis StartAbsoluteValue u EndAbsoluteValue Superscript m minus 2 Baseline u minus h left-parenthesis q right-parenthesis StartAbsoluteValue u EndAbsoluteValue Superscript l minus 2 Baseline u comma">

−

Δ

H

n

,

p
→

u
+
a
(
q
)

|

u

|

p
–

2

u
=
λ
w
(
q
)

|

u

|

m
−
2

u
−
h
(
q
)

|

u

|

l
−
2

u
,

-\Delta _{{\mathbb {H}^n},\overrightarrow {p}}u +a(q)|u|^{p^–2}u=\lambda w(q)|u|^{m-2}u-h(q)|u|^{l-2}u,

\]
in the Heisenberg group

H

n

{\mathbb {H}^n}

, where the operator

Δ

H

n

,

p
→

\Delta _{{\mathbb {H}^n},\overrightarrow {p}}

is the horizontal anisotropic

p
p

-Laplacian on the Heisenberg group and is defined in the sequel. By the variational methods, we prove the existence of the entire weak solutions.
Woronin body hitchhiking on early endosomes is dispensable for septal localization in Aspergillus nidulans
Authors: Songster Livia D. , Bhuyan Devahuti , Christensen Jenna R. , Reck-Peterson Samara L.
Published: April 2023

In the filamentous fungus Aspergillus nidulans, peroxisomes move by hitchhiking on early endosomes. Here, it is shown that the Woronin body, a peroxisome-derived organelle that plugs incomplete septa upon injury to hyphae, also hitchhikes on early endosomes. While hitchhiking is required for Woronin body distribution and motility, it is dispensable for septal localization and plugging.
WAVES (Web-based tool for Analysis and Visualization of Environmental Samples)—a web application for visualization of wastewater pathogen sequencing results
Authors: Triska Petr , Amman Fabian , Endler Lukas , Bergthaler Andreas
Published: April 2023

Motivation

Environmental monitoring of pathogens provides an accurate and timely source of information for public health authorities and policymakers. In the last 2 years, wastewater sequencing proved to be an effective way of detection and quantification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants circulating in population. Wastewater sequencing produces substantial amounts of geographical and genomic data. Proper visualization of spatial and temporal patterns in these data is crucial for the assessment of the epidemiological situation and forecasting. Here, we present a web-based dashboard application for the visualization and analysis of data obtained from sequencing of environmental samples. The dashboard provides multi-layered visualization of geographical and genomic data. It allows to display frequencies of detected pathogen variants as well as individual mutation frequencies. The features of WAVES (Web-based tool for Analysis and Visualization of Environmental Samples) for early tracking and detection of novel variants in the wastewater are demonstrated in an example of BA.1 variant and the signature Spike mutation S: E484A. WAVES dashboard is easily customized through the editable configuration file and can be used for different types of pathogens and environmental samples.

Availability and implementation

WAVES source code is freely available at https://github.com/ptriska/WavesDash under MIT license. A demo version of this application can be accessed at: https://wavesdashboard.azurewebsites.net/.
Finite mixtures of matrix variate Poisson-log normal distributions for three-way count data
Authors: Silva Anjali , Qin Xiaoke , Rothstein Steven J , McNicholas Paul D , Subedi Sanjeena
Published: April 2023

Motivation

Three-way data structures, characterized by three entities, the units, the variables and the occasions, are frequent in biological studies. In RNA sequencing, three-way data structures are obtained when high-throughput transcriptome sequencing data are collected for n genes across p conditions at r occasions. Matrix variate distributions offer a natural way to model three-way data and mixtures of matrix variate distributions can be used to cluster three-way data. Clustering of gene expression data is carried out as means of discovering gene co-expression networks.

Results

In this work, a mixture of matrix variate Poisson-log normal distributions is proposed for clustering read counts from RNA sequencing. By considering the matrix variate structure, full information on the conditions and occasions of the RNA sequencing dataset is simultaneously considered, and the number of covariance parameters to be estimated is reduced. We propose three different frameworks for parameter estimation: a Markov chain Monte Carlo-based approach, a variational Gaussian approximation-based approach, and a hybrid approach. Various information criteria are used for model selection. The models are applied to both real and simulated data, and we demonstrate that the proposed approaches can recover the underlying cluster structure in both cases. In simulation studies where the true model parameters are known, our proposed approach shows good parameter recovery.

Availability and implementation

The GitHub R package for this work is available at https://github.com/anjalisilva/mixMVPLN and is released under the open source MIT license.
eccDB: a comprehensive repository for eccDNA-mediated chromatin contacts in multi-species
Authors: Yang Min , Qiu Bo , He Guo-You , Zhou Jian-Yuan , Yu Hao-Jie , Zhang Yu-Ying , Li Yan-Shang , Li Tai-Song , Guo Jin-Cheng , Li Xue-Cang , Xie Jian-Jun
Published: April 2023

We developed the eccDB database to integrate available resources for extrachromosomal circular DNA (eccDNA) data. eccDB is a comprehensive repository for storing, browsing, searching, and analyzing eccDNAs from multispecies. The database provides regulatory and epigenetic information on eccDNAs, with a focus on analyzing intrachromosomal and interchromosomal interactions to predict their transcriptional regulatory functions. Moreover, eccDB identifies eccDNAs from unknown DNA sequences and analyzes the functional and evolutionary relationships of eccDNAs among different species. Overall, eccDB offers web-based analytical tools and a comprehensive resource for biologists and clinicians to decipher the molecular regulatory mechanisms of eccDNAs.

Availability and implementation

eccDB is freely available at http://www.xiejjlab.bio/eccDB.
SmoothT—a server constructing low-energy pathways from conformational ensembles for interactive visualization and enhanced sampling
Authors: Staritzbichler René , Ristic Nikola , Stapke Tülin , Hildebrand Peter W
Published: April 2023

Motivation

The SmoothT software and webservice offers the construction of pathways from an ensemble of conformations. The user provides an archive of molecule conformations in Protein Databank (PDB) format, from which a starting and a final conformation need to be selected. The individual PDB files need to contain an energy value or score, estimating the quality of the respective confirmation. Additionally, the user has to provide a root-mean-square deviation (RMSD) cut-off, below which conformations are considered neighboring. From this, SmoothT constructs a graph that connects similar conformations.

Results

SmoothT returns the energetically most favorable pathway within in this graph. This pathway is directly displayed as interactive animation using the NGL viewer. Simultaneously, the energy along the pathway is plotted, highlighting the conformation that is currently displayed in the 3D window.

Availability and implementation

SmoothT is available as webservice at: http://proteinformatics.org/smoothT. Examples, a tutorial, and FAQs can be found there. Ensembles up to 2 GB (compressed) can be uploaded. Results will be stored for 5 days. The server is completely free and requires no registration. The C++ source code is available at: https://github.com/starbeachlab/smoothT.
The Responsibility Team—A Way to Ensure Children’s Right to Participation?
Authors: Sæbjørnsen Siv Elin Nord , Larsen Bjørn Kjetil , Ødegård Atle
Published: April 2023

Children’s effective participation seems to be difficult to achieve in practice. Although the United Nations Convention on the Rights of the Child came into force in 1989, recent research reports that effective participation rarely occurs. This qualitative study explores a group of adolescents’ views on participating in child welfare ‘responsibility teams’ (RTs) in Norway. The two specific foci are experiences regarding influence on their own situation and how the RT model may be a useful way to ensure children’s right to participate. The study concludes that RT alone cannot ensure children’s right to participate in the form of effective participation and that professional competencies are also important. The study calls for further research, especially on children and adolescents’ own experiences with RTs.
Impact of the RNA allosteric effect triggered by single nucleotide polymorphisms on the splicing process
Authors: Zhuang Youyuan , Lu Xiaoyan , Lin Peng , Wang Siyu , Sheng Xiaoran , Chen Chong , Zhang Guosi , Wang Zhiyi , Mei Changqiu , Qu Jia , Xu Liangde , Wang Hong
Published: April 2023

The susceptibility single nucleotide polymorphisms (SNPs) obtained by genome-wide association studies leave some thorny questions, such as prioritization, false positives and unknown pathogenesis. Previous studies suggested that genetic variation may perturb the RNA secondary structure, influence protein recruitment and binding and ultimately affect splicing processes. Therefore, exploring the perturbation of SNPs to structure–function correlations may provide an effective bridge toward understanding the genetic contribution to diseases. Here, aiming to decipher the regulatory mechanism of myopia susceptibility variants, we systematically evaluated the roles of SNP-induced structural changes during splicing. In addition, 7.53% of myopia-related SNPs exhibited significant global structural changes, 19.53% presented noteworthy local structural disturbance and there were wide-ranging structural perturbations in the splice-related motifs. We established a comprehensive evaluation system for structural disturbance in the splicing-related motifs and gave the priority ranking for the SNPs at RNA structural level. These high-priority SNPs were revealed to widely disturb the molecular interaction properties between splicing-related proteins and pre-mRNAs by HDOCK. Moreover, mini-gene assays confirmed that structural perturbation could influence splicing efficiency through structural remodelling. This study deepens our understanding of the potential molecular regulatory mechanisms of susceptible SNPs in myopia and contributes to personalized diagnosis, personalized medicine, disease-risk prediction and functional verification study by guiding the prioritization of the susceptibility SNPs.
Resistance is common in paediatric patients failing ART in South Africa
Authors: Hunt Gillian M , Yousif Mukhlid , Levin Leon , Ledwaba Johanna , Steegen Kim , Kufa Tendesayi , Zwane Hloniphile , Kalimashe Monalisa , Kana Vibha , Aynalem Getahun , Perlman Jaclyn , Ayalew Kassahun , Kindra Gurpreet , Diallo Karidia , Carmona Sergio , Sherman Gayle , Raizes Elliot J
Published: April 2023

Background

Minimal data exist on HIV drug resistance patterns and prevalence among paediatric patients failing ART in resource-limited settings. We assessed levels of HIV drug resistance in children with virological failure.

Methods

This cross-sectional study, performed from March 2017 to March 2019 in South Africa, enrolled HIV-positive children aged ≤19 years, receiving ART through public health facilities with recent evidence suggestive of virological failure (at least one viral load ≥1000 copies/mL), across 45 randomly selected high-volume clinics from all nine provinces. Resistance genotyping was performed using next-generation sequencing technologies. Descriptive analysis taking into account survey design was used to determine outcomes.

Results

Among 899 participants enrolled, the adjusted proportion of HIV drug resistance among children with virological failure was 87.5% (95% CI 83.0%–90.9%). Resistance to NNRTIs was detected in 77.4% (95% CI 72.5%–81.7%) of participants, and resistance to NRTIs in 69.5% (95% CI 62.9%–75.4%) of participants. Overall, resistance to PIs was detected in 7.7% (95% CI 4.4%–13.0%) of children.

Conclusions

HIV drug resistance was highly prevalent in paediatric patients failing ART in South Africa, with 9 in 10 patients harbouring resistance to NNRTIs and/or NRTIs. PI-based regimens are predicted to be highly efficacious in achieving virological suppression amongst patients failing NNRTI-based regimens. Scaling up resistance testing amongst patients would facilitate access to second- and third-line regimens in South Africa.
Diagnostic Performance of Anti-dsDNA Tests by Indirect Immunofluorescence and Enzyme-linked Immunosorbent Assay in Patients with Systemic Lupus Erythematosus
Authors: Nieto-Aristizábal Ivana , España Laura Jackeline , Ortega Jorge , Ruiz-Ordoñez Ingrid , Vivas Álvaro J , Castaño Gloria L , Castillo Carmen , Bautista-Vargas Mario , Suárez Ana , Cañas Carlos A , Tobón Gabriel J
Published: April 2023

Background

Several laboratory techniques for anti double-stranded (ds) DNA detection in systemic lupus erythematosus (SLE) are available, with variable diagnostic performance. We aimed to evaluate anti-dsDNA’s diagnostic performance by indirect immunofluorescence (IIF) and enzyme-linked immunosorbent assay (EIA).

Methods

We conducted a single-center retrospective (2015 to 2020) study. Patients with anti-dsDNA tests by IIF and EIA were included. We evaluated the indications, applications, concordance, positive predictive value (PPV) of anti-dsDNA to confirm SLE diagnosis or flares, and associations of disease manifestations with positivity with each technique.

Results

A total of 1368 reports of anti-dsDNA tests by IIF and EIA and the corresponding medical records of the patients were analyzed. The main indication for anti-dsDNA testing was to help in the diagnosis of SLE in 890 (65%) of the samples, and the main application after obtaining the results was SLE exclusion in 782 (57.2%) cases. The combination with the highest frequency was the negativity result by both techniques in 801 (58.5%) cases (Cohen kappa 0.57). Both methods were positive in 300 patients with SLE (Cohen kappa 0.42). The PPVs of anti-dsDNA tests to confirm diagnosis/flare was 79.64% (95% CI, 75.35–83.35) by EIA, 78.75% (95% CI, 74.27–82.62) by IIF, and 82% (95% CI, 77.26–85.93) when both were positive.

Conclusions

Anti-dsDNA detection by IIF and EIA are complementary and may indicate different clinical patterns in patients with SLE. The detection of anti-dsDNA antibodies by both techniques has a higher PPV than either separately for confirming SLE diagnosis or flares. These results highlight the need for evaluating both methods in clinical practice.
Enhancing three-dimensional convolutional neural network-based geometric feature recognition for adaptive additive manufacturing: a signed distance field data approach
Authors: Hilbig Arthur , Vogt Lucas , Holtzhausen Stefan , Paetzold Kristin
Published: April 2023

In the context of additive manufacturing, the adjustment of process data to individual geometric features offers the potential to further increase manufacturing speed and quality, while being widely underestimated in recent research. Unfortunately, the current non-uniform data handling in the CAD-CAM-Link results in a downstream data loss, that prevents the availability of geometric knowledge from being present at any time to apply the more advanced approaches of adaptive slicing and tool path generation. Automatic detection of various geometric entities would be beneficial for classifying partial surfaces and volumetric ranges to gain customized informational insights of geometric parameterization. In this work, an enhanced approach of geometric deep learning for the analysis of voxelized engineering parts will be presented to align the inference representations to modeling paradigms for complex design models like architected materials. Although the baseline voxel representation offers distinct advantages in detection accuracy, it comes with an adversely large memory footprint. The geometry discretization leads to high resolutions needed to capture various detail levels that prevent the analysis of fine-grained objects. To achieve efficient usage of three-dimensional (3D) deep learning techniques, we propose a 3D-convolutional neural network-based feature recognition approach using signed distance field data to limit the needed resolution. These implicit geometric data leverage the advantages of volumetric convolution while alleviating their disadvantages through the use of the continuous signed distance function. When analyzing computer-aided design data for geometric primitive features, a common application task in surface reconstruction of reverse engineering the proposed methodology, achieves a detection accuracy that is in line with the accuracy values achieved by comparable algorithms. This enables the recognition of fine-grained surface instances. The unambiguous shape information extracted could be used in subsequent adaptive slicing algorithms to achieve individual geometry-based hatch generation.
Venetoclax plus low-dose cytarabine in patients with newly diagnosed acute myeloid leukemia ineligible for intensive chemotherapy: an expanded access study in Japan
Authors: Asada Noboru , Ando Jun , Takada Satoru , Yoshida Chikashi , Usuki Kensuke , Shinagawa Atsushi , Ishizawa Kenichi , Miyamoto Toshihiro , Iida Hiroatsu , Dobashi Nobuaki , Okubo Sumiko , Honda Hideyuki , Soshin Tomomi , Nishimura Yasuko , Tsutsui Atsuko , Mukai Harumi , Yamamoto Kazuhito
Published: April 2023

Background

In a Phase 3 international clinical trial (VIALE-C), venetoclax plus low-dose cytarabine improved the response rate and overall survival versus placebo plus low-dose cytarabine in patients with newly diagnosed acute myeloid leukemia who were ineligible for intensive chemotherapy. After the enrollment period of VIALE-C ended, we conducted an expanded access study to provide preapproval access to venetoclax in combination with low-dose cytarabine in Japan.

Methods

Previously, untreated patients with acute myeloid leukemia who were ineligible for intensive chemotherapy were enrolled according to the VIALE-C criteria. Patients received venetoclax (600 mg, Days 1–28, 4-day ramp-up in Cycle 1) in 28-day cycles and low-dose cytarabine (20 mg/m2, Days 1–10). All patients took tumor lysis syndrome prophylactic agents and hydration. Safety endpoints were assessed.

Results

Fourteen patients were enrolled in this study. The median age was 77.5 years (range = 61–84), with 78.6% over 75 years old. The most common grade ≥ 3 treatment-emergent adverse event was neutropenia (57.1%). Febrile neutropenia was the most frequent serious adverse event (21.4%). One patient developed treatment-related acute kidney injury, leading to discontinuation of treatment. Two patients died because of cardiac failure and disease progression that were judged not related to study treatment. No patients developed tumor lysis syndrome.

Conclusions

The safety outcomes were similar to those in VIALE-C without new safety signals and were well managed with standard medical care. In clinical practice, more patients with severe background disease are expected, in comparison with in VIALE-C, suggesting that it is important to carefully manage and prevent adverse events.
Congruent and Differential Responses of Pseudoperonospora cubensis Clades 1 and 2 to Downy Mildew Fungicides
Authors: Keinath Anthony P.
Published: April 2023

Fungicides are the most common and important management technique for cucurbit downy mildew. Fungicide efficacy against the causal agent Pseudoperonospora cubensis, an obligate biotroph, has been monitored on potted cucumber seedlings exposed to natural inoculum. The objective of this study was to compare the efficacy of nine fungicides on cucumber ( Cucumis sativus) against Clade 2 of P. cubensis with their efficacy on butternut squash ( Cucurbita moschata) and watermelon ( Citrullus lanatus), hosts primarily infected by Clade 1. Bioassays were done in Charleston, SC, United States, with all three hosts in October 2019 and 2020 and with butternut squash in July 2018. Lack of efficacy, determined as relative disease severity not significantly different from the water control, typically ≥50%, was detected with cymoxanil (Curzate), azoxystrobin (Quadris), dimethomorph (Forum), mandipropamid (Revus), or propamocarb (Previcur Flex) more frequently in Clade 2 isolates (7 of 18 times) than in Clade 1 isolates (12 of 43 times). Cymoxanil, azoxystrobin, and dimethomorph were ineffective in over half of the bioassays on all hosts. Mandipropamid was ineffective only against Clade 2 in both cucumber assays, whereas propamocarb was ineffective only against Clade 1 in two of three and one of two bioassays on butternut squash and watermelon, respectively. In all seven bioassays, ethaboxam (Elumin) was effective to moderately effective, and cyazofamid (Ranman), fluazinam (Omega), and fluopicolide (Presidio) were effective.