bluuebunny/crossref_metadata_2025 huggingface dataset:
Ambiguous genes due to aligners and their impact on RNA-seq data analysis
Authors: Szabelska-Beresewicz Alicja , Zyprych-Walczak Joanna , Siatkowski Idzi , Okoniewski Michał
Published: December 2023

The main scope of the study is ambiguous genes, i.e. genes whose expression is difficult to estimate from the data produced by next-generation sequencing technologies. We focused on the RNA sequencing (RNA-Seq) type of experiment performed on the Illumina platform. It is crucial to identify such genes and understand the cause of their difficulty, as these genes may be involved in some diseases. By giving misleading results, they could contribute to a misunderstanding of the cause of certain diseases, which could lead to inappropriate treatment. We thought that the ambiguous genes would be difficult to map because of their complex structure. So we looked at RNA-seq analysis using different mappers to find genes that would have different measurements from the aligners. We were able to identify such genes using a generalized linear model with two factors: mappers and groups introduced by the experiment. A large proportion of ambiguous genes are pseudogenes. High sequence similarity of pseudogenes to functional genes may indicate problems in alignment procedures. In addition, predictive analysis verified the performance of difficult genes in classification. The effectiveness of classifying samples into specific groups was compared, including the expression of difficult and not difficult genes as covariates. In almost all cases considered, ambiguous genes have less predictive power.
Linguistic characteristics in bipolar disorder versus borderline personality disorder
Authors: Muriel Noelia Santos , López Resa Patricia , Moraleda Sepúlveda Esther
Published: December 2023

Scientific evidence has documented throughout the research carried out in recent years, the neuropsychological, behavioral and adaptive difficulties presented by people with Bipolar Disorder and Borderline Personality Disorder at different stages of their development. However, little importance has been given to other factors such as communication, especially in the adult population. The objective of this research was to know the language characteristics presented by people from both groups and the differences in linguistic development. The sample consisted of 60 participants between the ages of 17 and 42:31 of them with a diagnosis of Borderline Personality Disorder and the remaining 29 with a diagnosis of Bipolar Disorder. The standardized evaluation instruments were: the Social Skills Scale and the Pragmatic Competence Questionnaire completed by three different informants (families, professionals and the own person). The results obtained show that both populations manifest linguistic difficulties in adulthood and that there are differences depending on the perception of the agent involved in the language assessment. These results are highly relevant since they provide up-to-date information about language level, support the need for language intervention in adulthood, and reflect a different communicative profile in Bipolar Disorder and Borderline Personality Disorder.
Elevation determines the productivity of large cardamom (Amomum subulatum Roxb.) cultivars in Sikkim Himalaya
Authors: Lepcha Patrush , Gaira Kailash S. , Pandey Aseesh , Chettri Santosh Kumar , Lepcha Jarina , Lepcha Jhony , Joshi Rajesh , Chettri Nakul
Published: December 2023

Large cardamom (Amomum subulatum Roxb.) is an economically important cash crop that provides a livelihood option for the rural communities in Sikkim Himalaya. However, its production has declined drastically over the past few decades due to climate change and other factors affecting the livelihood of marginal cardamom-dependent farmers in the region. Climate change causes a shift in elevational distributions of mountain species, and it is pivotal to understand its effect on yield and yield-related traits for economically important plant species like large cardamom. For this, we randomly studied 41 large cardamom cultivation sites in Sikkim (India) with elevations ranging between 975 and 2069 m asl and evaluated the yield-related traits (number of capsules per spike, capsule length, capsule width, fresh capsule weight, dry capsule weight, number of seeds per locule, fresh seed weight, and dry seed weight) in five cultivars (Dzongu Golsey, Sawney, Seremna, Ramsey, and Varlangey). We observed a significant variability (P < 0.05) for morphometric traits in each of the five cultivars cultivated in different elevations. The cultivation of low-elevation cultivars like Seremna and Dzongu Golsey (suitable in elevation < 975 m) has shifted upward to mid (975–1515 m) and high-elevation (> 1515 m), while cultivation of high-elevation Ramsey cultivar (suitable in elevation > 1515 m) has shifted downward (< 1515 m). The Dzongu Golsey, Sawney, and Seremna cultivated in mid-elevation (975–1515 m) performed better in terms of yield-related traits than the same cultivars cultivated in high-elevation (> 1515 m) and showed moderate to high negative correlation between elevation and yield-related traits, indicating the negative effect of elevation on their yield. Likewise, Ramsey and Varlangey cultivated in high elevation (> 1515 m) performed better than the one cultivated in mid-elevation (975–1515 m) and depicted moderate to high positive correlation between elevation and yield-related traits, suggesting a positive influence of elevation on their yield. Although there is an elevational shift in the cultivation of large cardamom cultivars, the elevation influences the performance of the large cardamom cultivars, and it also suggests cultivating the cultivars in their suitable elevation range for better productivity.
Integrating DNA methylation and gene expression data in a single gene network using the iNETgrate package
Authors: Sajedi Sogand , Ebrahimi Ghazal , Roudi Raheleh , Mehta Isha , Heshmat Amirreza , Samimi Hanie , Kazempour Shiva , Zainulabadeen Aamir , Docking Thomas Roderick , Arora Sukeshi Patel , Cigarroa Francisco , Seshadri Sudha , Karsan Aly , Zare Habil
Published: December 2023

Analyzing different omics data types independently is often too restrictive to allow for detection of subtle, but consistent, variations that are coherently supported based upon different assays. Integrating multi-omics data in one model can increase statistical power. However, designing such a model is challenging because different omics are measured at different levels. We developed the iNETgrate package (https://bioconductor.org/packages/iNETgrate/) that efficiently integrates transcriptome and DNA methylation data in a single gene network. Applying iNETgrate on five independent datasets improved prognostication compared to common clinical gold standards and a patient similarity network approach.
Despite misinformation, low trust, and conflict in Somalia, high demand for vaccines and a negative endorsement effect of non-state authorities
Authors: Aarslew Laurits F. , Haas Nicholas , Khadka Prabin B.
Published: December 2023

Expanding vaccination coverage in conflict regions is crucial to the prevention of further mutations and outbreaks of COVID-19, as well as of future pandemics, worldwide. However, scholars’ suppositions that low levels of trust and control over the flow of misinformation in these regions may necessitate tailored solutions—in particular, that health advice come from trusted non-state authorities—remain largely untested. To better understand the levels and drivers of COVID-19 vaccine receptivity in conflict regions, we partnered with the United Nations and the Somali Ministry of Justice to field a three-wave panel survey ($$N_1$$

N
1

= 1672; $$N_2$$

N
2

= 880; $$N_3$$

N
3

= 908) and vaccine endorsement experiment in South Central Somalia. We observe high overall demand for vaccines (between 90 and 94%), particularly among those who have experienced violence and illness, who perceive high economic disruption due to the pandemic, and who report more favorable views of and exposure to the West and Western-affiliated organizations. The high overall demand is particularly striking given respondents’ low interpersonal trust and considerable exposure to vaccine disinformation. Contrary to scholars’ and policymakers’ expectations, we find that whereas endorsements from government health authorities increase vaccine receptivity, endorsements from non-state customary authorities and extremist militant group Al-Shabaab decrease support for vaccination (− 8 and − 16% points, respectively). Our findings caution against presupposing a need for different approaches to increasing vaccination coverage in conflict regions, and suggest that at least in the short-term, constraints on vaccine supply and access are more likely to bind than those on demand.
Geographical distribution-based differentiation of cultivated Angelica dahurica, exploring the relationship between the secretory tract and the quality
Authors: Wu Qinghua , Jiang Lan , Yan Yuhang , Yan Qi , Zhu Xinglong , Zhang Jiaxu , Huang Chengfeng , Zhou Tao , Ren Chaoxiang , Wen Feiyan , Pei Jin
Published: December 2023

Based on geographical distribution, cultivated Chinese Angelica dahurica has been divided into Angelica dahurica cv. ‘Hangbaizhi’ (HBZ) and Angelica dahurica cv. ‘Qibaizhi’ (QBZ). Long-term geographical isolation has led to significant quality differences between them. The secretory structure in medicinal plants, as a place for accumulating effective constituents and information transmission to the environment, links the environment with the quality of medicinal materials. However, the secretory tract differences between HBZ and QBZ has not been revealed. This study aimed to explore the relationship between the secretory tract and the quality of two kinds of A. dahurica. Root samples were collected at seven development phases. High-Performance Liquid Chromatography (HPLC) and Desorption Electrospray Ionization Mass Spectrometry Imaging (DESI-MSI) were used for the content determination and spatial location of coumarins. Paraffin section was used to observe and localize the root secretory tract. Origin, CaseViewer, and HDI software were used for data analysis and image processing. The results showed that compared to QBZ, HBZ, with better quality, has a larger area of root secretory tracts. Hence, the root secretory tract can be included in the quality evaluation indicators of A. dahurica. Additionally, DESI-MSI technology was used for the first time to elucidate the temporal and spatial distribution of coumarin components in A. dahurica root tissues. This study provides a theoretical basis for the quality evaluation and breeding of improved varieties of A. dahurica and references the DESI-MSI technology used to analyze the metabolic differences of various compounds, including coumarin and volatile oil, in different tissue parts of A. dahurica.
Assessment of interobserver concordance in radiomic tools for lung nodule classification, with a focus on BRODERS and SILA
Authors: Al-Ghoula Faysal , Patel Khushbu , Falde Sam , Rajagopalan Srinivasan , Bartholmai Brian , Maldonado Fabien , Peikert Tobias
Published: December 2023

While CT lung cancer screening reduces lung cancer-specific mortality, there are remaining challenges. Radiomic tools promiss to address these challenges, however, they are subject to interobserver variability if semi-automated segmentation techniques are used. Herein we report interobserver variability for two validated radiomic tools, BRODERS (Benign versus aggRessive nODule Evaluation using Radiomic Stratification) and CANARY (Computer-Aided Nodule Assessment and Risk Yield). We retrospectively analyzed the CT images of 95 malignant lung nodules of the adenocarcinoma spectrum using BRODERS and CANARY. Cases were identified at Mayo Clinic (n = 45) and Vanderbilt University Medical Center and Nashville/Veteran Administration Tennessee Valley Health Care System (n = 50). Three observers with different training levels (medical student, internal medicine resident and thoracic radiology fellow) each performed lung nodule segmentation. All methods were carried out in accordance with relevant guidelines and regulations. Interclass correlation coefficients (ICC) of 0.77, 0.98 and 0.97 for the average nodule volume, BRODERS cancer probability and Score Indicative of Lesion Aggression (SILA) which summarizes the distribution of the CANARY exemplars indicated good to excellent reliability, respectively. The dice similarity coefficient was 0.79 and 0.81 for the data sets from the two institutions. BRODERS and CANARY are robust radiomics tools with excellent interobserver variability. These tools are simple and reliable regardless the observer/operator’s level of training.
Imaging of vertical surface-breaking cracks in concrete members using ultrasonic shear wave tomography
Authors: Kuchipudi Sai Teja , Pudovikov Sergey , Wiggenhauser Herbert , Ghosh Debdutta , Rabe Ute
Published: December 2023

Surface-breaking cracks in concrete pose a significant threat to the durability of built structures. They create pathways for an accelerated moisture intrusion, and the transport of environmental and chemical agents such as chloride ions, which in turn, exacerbate reinforced concrete deterioration. Estimating the extent of crack propagation beneath the surface helps in determining the safety, durability and reliability of a structure. This information can be used to devise appropriate repair methodologies. Developments in Dry Point Contact (DPC)-based ultrasonic arrays have enabled the detection and localization of defects in concrete through high-resolution imaging. This work proposes the use of Half-Skip travel modes in the time-domain pulse-echo data to be deployed for imaging vertical cracks in concrete. In contrast to the standard Synthetic Aperture Focusing Technique (SAFT), which is widely used for ultrasonic imaging of concrete, the Half-Skip Total Focusing Method (HSTFM) configuration uses the target-scattered signals after a reflection from the back wall. The technique has been evaluated on both simulated and experimentally measured ultrasonic data on specimens fabricated with notches and cracks of different depths. Crack sizes were estimated by measuring the length of thresholded reflection signatures obtained in the images. The presented solution using half-skip modes serves as a supplementary technique to standard SAFT, in order to estimate the depth of surface-breaking cracks in concrete.
Experience sampling reveals the role that covert goal states play in task-relevant behavior
Authors: Mckeown Brontë , Strawson Will H. , Zhang Meichao , Turnbull Adam , Konu Delali , Karapanagiotidis Theodoros , Wang Hao-Ting , Leech Robert , Xu Ting , Hardikar Samyogita , Bernhardt Boris , Margulies Daniel , Jefferies Elizabeth , Wammes Jeffrey , Smallwood Jonathan
Published: December 2023

Cognitive neuroscience has gained insight into covert states using experience sampling. Traditionally, this approach has focused on off-task states. However, task-relevant states are also maintained via covert processes. Our study examined whether experience sampling can also provide insights into covert goal-relevant states that support task performance. To address this question, we developed a neural state space, using dimensions of brain function variation, that allows neural correlates of overt and covert states to be examined in a common analytic space. We use this to describe brain activity during task performance, its relation to covert states identified via experience sampling, and links between individual variation in overt and covert states and task performance. Our study established deliberate task focus was linked to faster target detection, and brain states underlying this experience—and target detection—were associated with activity patterns emphasizing the fronto-parietal network. In contrast, brain states underlying off-task experiences—and vigilance periods—were linked to activity patterns emphasizing the default mode network. Our study shows experience sampling can not only describe covert states that are unrelated to the task at hand, but can also be used to highlight the role fronto-parietal regions play in the maintenance of covert task-relevant states.
Distal oblique bundle influence on distal radioulnar joint stability: a biomechanical study
Authors: Hohenberger G. , Pirrung F. , Hammer N. , Niestrawska J. A.
Published: December 2023

Chronic instability of the distal radioulnar joint (DRUJ) presents a highly disabling condition. Several surgical techniques have been reported for its treatment. These involve reconstruction of the distal oblique bundle (DOB) of the interosseous membrane (IOM) of the forearm. The aim of this study was to examine whether surgical reconstruction of the DOB is necessary to restore DRUJ stability following trauma with DOB disruption and to compare two restoration techniques utilizing a tendon or suture-button graft. Stability in supination and pronation was assessed by means of maximum torque and force in twenty forearms. Test cycles were performed with the DOB/IOM in an intact condition, with the DOB or distal IOM transected, and following surgical reconstruction of the DOB with either tendon graft or suture-button system. In pronation, the relative change in maximum axial force was significantly lower in samples with a transected DOB in comparison to samples without a preexisting DOB. No statistically significant differences were observed between forearms including DOB reconstruction and specimens in the intact and transected state. Neither were there statistically significant differences concerning the two surgical techniques. From a biomechanical perspective, surgical DOB reconstruction is hence not indicated in cases of isolated DOB rupture.
HER2 low expression breast cancer subtyping and their correlation with prognosis and immune landscape based on the histone modification related genes
Authors: Li Jia , Yao Jingchun , Qi Liqiang
Published: December 2023

Human epidermal growth factor receptor 2 (HER2) plays an important role in diagnosis and treatment of breast cancer (BRCA). The histone modification has been found to be related to the progression of cancer. This study aimed to probe the low HER2 expression BRCA heterogeneity by histone modification genes. The BRCA data and cell lines were collected from The Cancer Genome Atlas database. Weighted gene co-expression network analysis and non-negative matrix factorization clustering were jointly applied to obtain BRCA clusters. The expression of hub histone modification gene was detected using western blot assay. The gene ontology term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed to reveal functional information. The overall survival analysis was performed using survival and survminer packages, and the immune landscape was mainly analyzed using CIBERSORT software. Totally 43 histone modification genes correlated with survival of BRCA patients with HER2 low expression were screened. Based on these 43 histone modification genes, the BRCA samples were classified into cluster1, cluster2 and cluster3. Histone modification gene NFKBIZ exhibited high expression, while RAD51 demonstrated low expression in low HER2 expression BRCA cell. Cluster1 exhibited the best prognosis, while cluster3 had the worse outcomes. Tumor mutational burden (TMB) was remarkably increased in cluster3 group compared to cluster1 and cluster2. Moreover, the relative proportion of 16 immune cell infiltration and 8 immune checkpoint expression were remarkably differential among cluster1, cluster2 and cluster3, and the drug sensitivity exhibited difference among cluster1, cluster2 and cluster3 in BRCA patients with low HER2 expression. This study identified three HER2 low expression BRCA clusters with different characteristics based on histone modification genes. The TMB, immune cell infiltration, immune checkpoints and drug sensitivity were different among the three clusters.
Research on double camouflage encryption mechanism of QR code based on UAV landing scenario
Authors: Ye Hualong , Xu Tongxu
Published: December 2023

Usually, the landing area of the drone is presented with QR code images, so it is crucial to ensure the information security of the landing area and prevent it from being occupied by other users. This paper proposes a double camouflage encryption method of QR code based on UAV landing scenario. For the QR code image required for UAV landing, the private key and carrier image are used to complete double camouflage encryption, and then the public key is modulated according to the principle of ghost imaging to obtain the ciphertext. After receiving the ciphertext, the receiver first decrypts the camouflage image according to the public key, and then decrypts the QR code image using the private key. The UAV receives ciphertext information through the detector, for non-users, the correct QR code image cannot be decrypted through the wrong key. Even if the eavesdropper obtains the public key information, they can only decrypt the camouflage image and cannot land. For our users, the public key and the double private key can decrypt the correct QR code image for landing. This encryption method can effectively decrypt the image at non-full sampling rate, while also resisting the external noise attack, and has high security.
Additively manufactured magic cube platforms for fully integrated wireless sensing nodes for Internet of Things applications
Authors: Holda Madeline Elaine , Lynch Charles , Tentzeris Manos M.
Published: December 2023

Wireless sensor networks for environmental monitoring are a key feature in developing the Internet of Things. Although there has been much research in developing components for wireless sensing nodes, advances in creating fully integrated sensing nodes is limited. Furthermore, because most sensing nodes that have been developed are intended to perform a fixed task, each new effort to design an integrated sensing node with different functionality must start from scratch. Here we introduce a broadly applicable platform for the development and production of fully integrated wireless sensing nodes. The platform is an additively manufactured cube that has different subsystems occupying separate faces of the 3D structure. While both additively manufactured sensors and cube-shaped wireless sensing nodes have been previously reported, these two approaches have yet to be combined. A key technology that enables this is the use of additively manufactured, nonplanar bent microstrips. This realization offers a “plug-and-play” approach to sensor node design, as the subsystems are considered modular and can be swapped to alter the function of the device. Implementing this concept enables the rapid development and deployment of wireless sensor networks.
Comparing the seoi-nage skill of elite and non-elite judo athletes
Authors: Choi Sang-Hyup , Song Yong-Gwan
Published: December 2023

Seoi-nage performance requires a high level of skill and proficiency. The aim of this study was to compare the motor planning, regulation, and control skills of elite versus non-elite seoi-nage judo athletes. Twenty subjects (10 elites and 10 non-elite) performed the three-phase seoi-nage skills of unbalancing, positioning, and throwing while an optical motion capture 3D camera monitored their shoulder, pelvis, hip, and knee joint movements to calculate their force magnitude and direction. Elite athletes performed better than non-elite athletes in terms of the shoulder (247.4° vs. 208.3° in Event 4) and pelvic (235.4° vs. 194.4° in Event 4) rotation, tilt angle (15.13° vs. − 0.74° in Event 4) characteristics, as well as hip (136.1° vs. 125.0° in Event 4) and knee joint (124.0° vs. 120.8° in Event 3) flexion–extension angle. Compared to non-elite athletes, elite athletes also showed more controlled force and movement in all bodily areas. These results can help to guide the development of seoi-nage skills as judo athletes advance from the non-elite to the elite level.
Fisheries subsidies exacerbate inequities in accessing seafood nutrients in the Indian Ocean
Authors: Andreoli Vania , Meeuwig Jessica J. , Skerritt Daniel J. , Schuhbauer Anna , Sumaila U. Rashid , Zeller Dirk
Published: December 2023

Harmful, capacity-enhancing subsidies distort fishing activities and lead to overfishing and perverse outcomes for food security and conservation. We investigated the provision and spatial distribution of fisheries subsidies in the Indian Ocean. Total fisheries subsidies in the Indian Ocean, estimated at USD 3.2 billion in 2018, were mostly harmful subsidies (60%), provided to the large-scale industrial sector by mainly a few subsidising countries, including Distant Water Fishing countries. We also explored possible socio-economic drivers of the composition of subsidies, and show that the extent of harmful subsidies provided by Indian Ocean Rim (IOR) countries to their industrial sector can be predicted by the seafood export quantities of these countries. These results illustrate the inequity in accessing fisheries resources for the small-scale sector of nutrient insecure and ocean-dependant IOR countries. The present study can benchmark future assessments and implementation of fisheries subsidy disciplines in the region following the World Trade Organisation Agreement on Fisheries Subsidies.
Application of plutonium radiochronometry to understand material processing impacts for nuclear forensics
Authors: Higginson Matthew A. , Gilligan Christopher R. D. , Dawkins Brogen , Kaye Philip
Published: December 2023

Radiochronometry is a key measurement aimed to determine the model age of an unknown sample for nuclear forensics. Analysis of decay products in materials of known provenance is crucial to allow us to confidently assess how fuel cycle processes impact forensic signatures. Measurement of multiple chronometers allows for a nuanced sample history to be interpreted. In this work we apply our analytical capabilities to two materials of known provenance to further validate our understanding specifically aiming to understand wet chemistry, feedstock blending and the impacts of thermal processing on plutonium samples. In addition to the actinide decay progeny measurements, the 4He chronometer is shown to have utility for materials with complex processing histories.
Application of radiocaesium microscale observation methodology to parmelioid lichen and ultrastructural analyses using STEM-EDS
Authors: Dohi Terumi , Iijima Kazuki , Machida Masahiko , Suno Hiroya , Ohmura Yoshihito , Fujiwara Kenso , Kimura Sigeru , Kanno Futoshi
Published: December 2023

A method to examine the localisation of radiocaesium in lichen thallus tissues using autoradiography was applied to the parmelioid lichen, Punctelia borreri, collected six years after the Fukushima Dai-ichi nuclear power plant accident. Radiocaesium was detected in the lower cortex of thallus tissues and associated rhizines that contained brown melanin-like pigment. This finding was consistent with our previous findings for the lichen Parmotrema tinctorum. In addition, we observed the ultrastructure of upper cortex tissue within Parmotrema tinctorum using STEM-EDS analysis, where a sub-micron particle was found to be present inside the tissue. The presence of radiocaesium particles in the cortex matrix of the lichen, similar to other sub-micron particles, may be a factor in the long-term retention capability of radionuclides within lichens.
Determination of Blue Carbon sequestration rates in the UK North Sea using lead-210 and complementary fingerprinting tools
Authors: Dal Molin Franck , Blowers Paul , Brady Daniel , Brown Nathan , Cogan Stephanie , Davis Terri , Hamstead Peter , Huk Mariusz , Limbach Hannah , Smedley Paul
Published: December 2023

The fallout of lead-210 (210Pb), present naturally in the atmosphere from the decay of radon gas, is a source of information that is commonly utilised to estimate time-trends of relatively recent environmental changes, variations and pressures recorded in aquatic sediment cores. Over the last four decades, this geochronological tool has been utilised in diverse environmental research applications. Currently in the United Kingdom (UK), there is a particular growing demand from marine scientists interested in further understanding the sequestration rates of natural sources of organic carbon, also known as Blue Carbon (BC), that help mitigate the effect of climate change. Between 2021 and 2022, several surveys were undertaken in different coastal and offshore regions of the UK North Sea. These presented an opportunity to test different sample preparative and analytical approaches for measuring 210Pb and radium-226 (226Ra) in marine sediments, review the most important challenges and limitations when applying this geochronological tool in this marine region and investigate the best fingerprinting options available that could help validate results obtained from 210Pb-based modelling.
Studies on distribution of 210Po and 210Pb activity and physico chemical effects of undisturbed alluvial clay soil in Belagavi district, Karnataka, India
Authors: Kamalakar V. , Vinutha P. , Achari S. , Narayana Y.
Published: December 2023

The paper discusses the activity of 210Po and 210Pb and physico chemical effects on undisturbed alluvial clay soil in Belagavi district of Karnataka, India. The activity of 210Pb was estimated through 210Po by radiochemical separation and subsequent deposition on a silver disc. The α-activity was then counted using a ZnS(Ag) counter of 30% efficiency, and the activity was calculated. While the average of 210Po activity in soil samples ranged from 9.45 to 31.75 Bq kg−1, with an average of 16.76 Bq kg−1,Whereas, the 210Pb activity range from 17.58 to 78.52 Bq kg−1, with an average value of 37.89 Bq kg−1. 210Po and 210Pb activity ratio range from 0.39 to 0.54, with an average value of 0.46. The low activity of 210Po and 210Pb was observed in the dissolved phase due to the removal of these reactive radionuclides from solution. The granulometric contents (silt, clay, and sand), organic matter and pH contents were measured in soil, respectively. Using IBM SPSS software, a good correlation with correlation coefficient was found between the activity 210Po, and 210Pb with organic matter percentage and clay. The Surfer software version 8, kriging interpolation method, 3D map is used to predict the value of a random variable over a spatial region.
Electron Paramagnetic Resonance in Structural Biology
Authors: Bogdanov Alexey , Goldfarb Daniella
Published: December 2023

This chapter presents the application of electron paramagnetic resonance (EPR) spectroscopy to exploring the structure and dynamics of biomolecules, primarily proteins. Emphasis is given to pulsed dipolar EPR (PD-EPR), which provides distance distributions, typically in the range of 1.5–8 nm. Such measurements, usually carried out at low temperatures on frozen samples, are well established in solution and have been demonstrated as effective for in-cell studies. The chapter begins with a brief description of continuous wave EPR, followed by the most commonly used PD-EPR techniques, along with the associated data analysis methodology. Since most biomolecules are diamagnetic, site-directed spin labeling plays an essential role in EPR applications. The various spin labels currently available are discussed next. This is followed by a description of approaches used to model the rotational freedom of the spin label upon binding to specific sites in known structures and a prediction of the ensuing distance distribution. Then the use of distance distributions as constraints in structural derivation is briefly presented. The chapter concludes by showing some examples of the concurrent use of EPR techniques with other biophysical methods, such as NMR, SAXS, smFRET, and cryo-EM, highlighting actual biological applications, rather than model proteins often used for new method development.
Solid-state NMR-based Integrative Structural Methods for Protein and Viral Assemblies
Authors: Lusky Orr S. , Goldbourt Amir
Published: December 2023

Viruses and other protein assemblies are made of symmetric arrangements of biological macromolecules such as proteins, polynucleic acids, and fatty acids. In order to obtain an atomic resolution view of the complete structures of such systems a set of structural tools must be used. Those include predominantly X-ray crystallography, cryo-electron microscopy, solution- and solid-state NMR. Additional techniques such as small angle scattering and molecular dynamics may aid and complement those methods. Each of the techniques has advantages and drawbacks and when integrated together provide a more comprehensive and accurate description of complex biological systems. Solid-state NMR has emerged as a highly useful technique to study complex biomolecular assemblies with many applications to viruses, virus like particles, and protein assemblies. We demonstrate in this chapter how the combination of solid-state NMR with additional structural biology techniques can enrich and complement the atomic-resolution structural description of such systems.
Mechanistic Studies of Membrane Proteins Using Integrated Solid-state NMR and Computational Approaches
Authors: Mohr Swantje , Aldakul Yessenbek K. , Sun Han , Sawczyc Henry , Lange Adam
Published: December 2023

In structural biology, integrated approaches are often used to investigate complex systems. Membrane proteins, as one example of these systems, are a particularly important class of biomolecules, with their structure, dynamics, and function being dependent on the lipid environment they are embedded in. Solid-state NMR is one of a few techniques able to analyze those biomolecules in their native surroundings and under physiological conditions. Complemented by a variety of different molecular dynamics (MD) simulation-based techniques, many different protein systems can be characterized in detail regarding not only their structure, but also their interactions with other proteins, the environment, or small molecules. In this chapter, we describe a combination of solid-state NMR and MD simulations to characterize the structure and function of membrane proteins, focusing on ion channels and rhomboid proteases as two representative examples, and give an outlook on future perspectives in the field.
Synthesis of dimpled polymer–silica nanocomposite particles by interfacial swelling-based seeded polymerization
Authors: Yin Yiping , Wang Zhe , Zou Hua
Published: December 2023

Dimpled polymer–silica nanocomposite particles have the combined advantages of dimpled particles and polymer–silica nanocomposite particles.
Visible light-induced hydrogen atom transfer trifluoromethylthiolation of aldehydes with bismuth catalyst
Authors: Dong Jun , Tang Zhuang , Zou Luqian , Zhou Yongyun , Chen Jingchao
Published: December 2023

By using a combination of BiCl3 and TBACl as a ligand-to-metal charge transfer (LMCT) photocatalyst, hydrogen atom transfer trifluoromethylthiolation of aldehydes was achieved under visible light irradiation.
Benchmarking non-adiabatic quantum dynamics using the molecular Tully models
Authors: Gómez Sandra , Spinlove Eryn , Worth Graham
Published: December 2023

The on-the-fly direct dynamics variational multi-configuration Gaussian (DD-vMCG) method is validated using the Ibele–Curchod model molecular systems: ethene, DMABN and fulvene.
Interactions and reactivity in crystalline intermediates of mechanochemical cyclorhodation reactions
Authors: Gómez Sara , Gómez Santiago , Rojas-Valencia Natalia , Hernández José G. , Ardila-Fierro Karen J. , Gómez Tatiana , Cárdenas Carlos , Hadad Cacier , Cappelli Chiara , Restrepo Albeiro
Published: December 2023

State of the art computations help explain the differences in reactivity between transient cocrystals that precede the mechanochemical activation of C–H bonds during the formation of rhodacyles.
First principles study of a triazine-based covalent organic framework as a high-capacity anode material for Na/K-ion batteries
Authors: Liu Sitong , Liu Bo , Yu Meidong , Gao Hanyu , Guo Haipeng , Jiang Daguo , Yang Shenbo , Wen Yufeng , Wu Yabei
Published: December 2023

The low Na+/K+ diffusion barrier, high theoretical-capacity and shallow averaged open-circuit-voltage make bilayer triazine-based covalent organic frameworks a promising anode for NIBs and KIBs.
Can tunneling current in molecular junctions be so strongly temperature dependent to challenge a hopping mechanism? Analytical formulas answer this question and provide important insight into large area junctions
Authors: Bâldea Ioan
Published: December 2023

The single level model predicts that tunneling current can varies with temperature over several of magnitudes, challenging thereby the hopping mechanism, and is able to estimate the number of current carrying molecules in large area junctions.
Highly chemoselective and fast practical visible photoreduction of nitroaromatic compounds to aromatic amines and amides using a self-assembled triad TiO2-TEOA-NC (LMCT/EDA) complex system
Authors: Bagheri Natanzi Mahshid , Kazemi Foad , Zand Zahra , Kaboudin Babak
Published: December 2023

The triad TiO2-TEOA-NC (LMCT/EDA) complex system was self-assembled and used as a heterosupramolecular nano device in fast practical reduction of nitro compounds under visible light irradiation.
Precise and accurate isotopic analysis of uranium and thorium in uranium ore concentrates using ICP-MS and their age dating for nuclear forensic analysis
Authors: Wang Wei , Xu Jiang , Xi Ruiyang , Guo Siqi , Su Yongyang , Fang Sui , Zhang Haitao , Wang Yalong , Fan Jinlong , Feng Lei , Wang Yufeng , Li Zhiming
Published: December 2023

Precise and accurate analysis of 235U/238U, 234U/238U, 230Th/234U and 230Th/232Th in 15 uranium ore concentrates (UOCs) was achieved using ICP-MS for nuclear forensic applications. A novel method was developed to dating UOCs.
Facile access to 1,2-disubstituted benzimidazoles and 2,3-dihydro-1H-perimidines using a biogenically synthesized single phase δ-MnO2 NP catalyst and its dye removal study
Authors: R. Nandini , R. Thrilokraj , Kshirsagar Umesh A. , Hegde Rajeev V. , Ghosh Arnab , Patil Siddappa A. , Malecki Jan Grzegorz , Dateer Ramesh B.
Published: December 2023

The synthesis of single phase δ-MnO2 NPs was carried out utilising an environmentally benign biogenic method. The prepared catalyst was utilized for benzimidazoles and dihydroperimidines synthesis and the dye removal study with exceptional catalytic activity.
Two new 6-nitrobenzimidazole ligand-modified polymolybdate-based metal–organic complexes with excellent capacitive and electrocatalytic performances
Authors: Liang Ju-Ju , Zhang Yu-Chen , Chang Zhi-Han , Chen Yong-Zhen , Chen Ke-Ke , Lu Jun-Jun , Wang Xiu-Li
Published: December 2023

6-Nitrobenzimidazole ligand was first introduced into polyoxometalate-based metal–organic architecture, and two unique butterfly-like complexes were obtained. Their applications in electrochemical energy storage and electrocatalysis were studied.
Biochemical Society Science Communication Prize 2023
Authors: Heath Catherine
Published: December 2023

For the past 12 years, the Biochemical Society has looked to identify and celebrate outstanding science communication by young people, with an annual Science Communication Prize. This year, the competition was open to students studying for A-level/T-level/BTEC National/Scottish Highers or equivalent qualifications and students in higher education. We were looking for creative and engaging entries aimed at the general public, in both written and media categories.
Study on the production of Sophorolipid by Starmerella bombicola yeast using fried waste oil fermentation
Authors: Wang Haifeng , Gao Ruifang , Song Xin , Yuan Xiangdong , Chen Xiuli , Zhao Yanling
Published: December 2023

Sophorolipids (SLs) are surface active compounds that have excellent surface-lowering properties. SLs were produced by Starmerella bombicola (CGMCC1576) yeast with sunflower seed oil, fried waste oil, cooked tung oil and raw tung oil used as hydrophobic carbon sources. The results showed that the strain could use sunflower seed oil and fried waste oil as hydrophobic carbon sources to produce SLs, and the yields were 44.52 and 39.09 gl−1. It could not be used as cooked tung oil and raw tung oil. The analysis by high-performance liquid chromatography/high resolution mass spectrometry (HPLC-MS/MS) showed that the main composition and structure of SLs produced by fermentation using fried waste oil were similar to that of sunflower seed oil as hydrophobic carbon source. The yield of SLs was the highest when the fried waste oil was used as hydrophobic carbon source, glucose (8%), waste oil (6%) and yeast (0.3%). When fried waste oil was used as a hydrophobic carbon source in a parallel 4-strand fermentation tank (FT), the combination with the largest yield and the most cost saving was that 3% of fried waste oil was added into the initial medium, and another 3% was again added after 72 h of fermentation. The total yield of SLs was 121.28 gl−1, and the yield of lactone SLs was 48.07 gl−1.
Implementation and laboratory verification of method utilizing phase and neutral quantities for detection and location of low‐current earth faults in resonant grounded networks
Authors: Treider Thomas , Høidalen Hans Kristian
Published: December 2023

Earth faults is a challenging fault type to locate in resonant grounded networks due to their naturally low fault current, and the problem increases with an increased fault impedance. This paper describes the detailed implementation and laboratory testing of a method for detection, location and clearing of earth faults with very small fault currents. The method consists of two indicators used in the fault detection stage, where their simultaneous operation ensures selective fault detection and faulty feeder selection. One of these indicators also enables continuous fault indication throughout a sectionalizing process. The laboratory tests demonstrate that both indicators function as intended, and it is the current sensors which ultimately limit the attainable sensitivity. Faults up to 15 kΩ were detected successfully in the laboratory network based on phase current measurements, while the sectionalizing indicator showed much higher sensitivity and functioned as intended in a 50 kΩ fault. Measurements from one field test in a 22 kV network corroborate the laboratory results and demonstrate the expected earth fault indicator response.
Galaxy morphology from z ∼ 6 through the lens of JWST
Authors: Huertas-Company M. , Iyer K. G. , Angeloudi E. , Bagley M. B. , Finkelstein S. L. , Kartaltepe J. , McGrath E. J. , Sarmiento R. , Vega-Ferrero J. , Arrabal Haro P. , Behroozi P. , Buitrago F. , Cheng Y. , Costantin L. , Dekel A. , Dickinson M. , Elbaz D. , Grogin N. A. , Hathi N. P. , Holwerda B. W. , Koekemoer A. M. , Lucas R. A. , Papovich C. , Pérez-González P. G. , Pirzkal N. , Seillé L.-M. , de la Vega A. , Wuyts S. , Yang G. , Yung L. Y. A.
Published: December 2023

Context. The James Webb Space Telescope’s (JWST’s) unprecedented combination of sensitivity, spatial resolution, and infrared coverage has enabled a new era of galaxy morphology exploration across most of cosmic history.

Aims. We analyze the near-infrared (NIR ∼ 0.8 − 1 μm) rest-frame morphologies of galaxies with log M*/M⊙ > 9 in the redshift range of 0 < z < 6, compare with previous HST-based results and release the first JWST-based morphological catalog of ∼20 000 galaxies in the CEERS survey.

Methods. We classified the galaxies in our sample into four main broad classes: spheroid, disk+spheroid, disk, and disturbed, based on imaging with four filters: F150W, F200W, F356W, and F444W. We used convolutional neural networks (CNNs) trained on HST/WFC3 labeled images and domain-adapted to JWST/NIRCam.

Results. We find that ∼90% and ∼75% of galaxies at z < 3 have the same early and late and regular and irregular classification, respectively, in JWST and HST imaging when considering similar wavelengths. For small (large) and faint objects, JWST-based classifications tend to systematically present less bulge-dominated systems (peculiar galaxies) than HST-based ones, but the impact on the reported evolution of morphological fractions is less than ∼10%. Using JWST-based morphologies at the same rest-frame wavelength (∼0.8 − 1 μm), we confirm an increase in peculiar galaxies and a decrease in bulge-dominated galaxies with redshift, as reported in previous HST-based works, suggesting that the stellar mass distribution, in addition to light distribution, is more disturbed in the early Universe. However, we find that undisturbed disk-like systems already dominate the high-mass end of the late-type galaxy population (log M*/M⊙ > 10.5) at z ∼ 5, and bulge-dominated galaxies also exist at these early epochs, confirming a rich and evolved morphological diversity of galaxies ∼1 Gyr after the Big Bang. Finally, we find that the morphology-quenching relation is already in place for massive galaxies at z > 3, with massive quiescent galaxies (log M*/M⊙ > 10.5) being predominantly bulge-dominated.
Observational study of intermittent solar jets:p-mode modulation
Authors: Cai Qiuzhuo , Ruan Guiping , Zheng Chenxi , Schmieder Brigitte , Guo Jinhan , Chen Yao , Su Jiangtao , Liu Yang , Liu Jihong , Cao Wenda
Published: December 2023

Aims.Recurring jets are observed in the solar atmosphere. They can erupt intermittently over a long period of time. By the observation of intermittent jets, we wish to understand what causes the characteristics of the periodic eruptions.

Methods.We report intermittent jets observed by the Goode Solar Telescope (GST) with the TiO Broadband Filter Imager (BFI), the Visible Imaging Spectrometer (VIS) in Hα, and the Near-InfraRed Imaging Spectropolarimeter (NIRIS). The analysis was aided and complemented by 1400 Å and 2796 Å data from the Interface Region Imaging Spectrograph (IRIS). These observational instruments allowed us to analyze the temporal characteristics of the jet events. By constructing the Hαdopplergrams, we found that the plasma first moves upward, but during the second phase of the jet, the plasma flows back. Working with time slice diagrams, we investigated the characteristics of the jet dynamics.

Results.The jet continued for up to 4 h. The time-distance diagram shows that the peak of the jet has clear periodic-eruption characteristics (5 min) during 18:00 UT–18:50 UT. We also found a periodic brightening phenomenon (5 min) during the jet bursts in the observed bands in the transition region (1400 Å and 2796 Å), which may be a response to intermittent jets in the upper solar atmosphere. The time lag is 3 min. Evolutionary images in the TiO band revealed a horizontal movement of the granulation at the location of the jet. By comparison to the quiet region of the Sun, we found that the footpoint of the jet is enhanced at the center of the Hαspectral line profile, without significant changes in the line wings. This suggests prolonged heating at the footpoint of the jet. In the mixed-polarity magnetic field region of the jet, we observed the emergence of magnetic flux, its cancellation, and shear, indicating possible intermittent magnetic reconnection. This is confirmed by the nonlinear force-free field model, which was reconstructed using the magneto-friction method.

Conclusions.The multiwavelength analysis indicates that the events we studied were triggered by magnetic reconnection that was caused by mixed-polarity magnetic fields. We suggest that the horizontal motion of the granulation in the photosphere drives the magnetic reconnection, which is modulated byp-mode oscillations.