bluuebunny/crossref_metadata_2025 huggingface dataset:
Preparatory movement state enhances premovement EEG representations for brain–computer interfaces
Authors: Zhang Yuxin , Li Mengfan , Wang Haili , Zhang Mingyu , Xu Guizhi
Published: May 2024

Objective. Motor-related brain–computer interface (BCI) have a broad range of applications, with the detection of premovement intentions being a prominent use case. However, the electroencephalography (EEG) features during the premovement phase are not distinctly evident and are susceptible to attentional influences. These limitations impede the enhancement of performance in motor-based BCI. The objective of this study is to establish a premovement BCI encoding paradigm that integrates the preparatory movement state and validates its feasibility in improving the detection of movement intentions. Methods. Two button tasks were designed to induce subjects into a preparation state for two movement intentions (left and right) based on visual guidance, in contrast to spontaneous premovement. The low frequency movement-related cortical potentials (MRCPs) and high frequency event-related desynchronization (ERD) EEG data of 14 subjects were recorded. Extracted features were fused and classified using task related common spatial patterns (CSP) and CSP algorithms. Differences between prepared premovement and spontaneous premovement were compared in terms of time domain, frequency domain, and classification accuracy. Results. In the time domain, MRCPs features reveal that prepared premovement induce lower amplitude and earlier latency on both contralateral and ipsilateral motor cortex compared to spontaneous premovement, with susceptibility to the dominant hand’s influence. Frequency domain ERD features indicate that prepared premovement induce lower ERD values bilaterally, and the ERD recovery speed after button press is the fastest. By using the fusion approach, the classification accuracy increased from 78.92% for spontaneous premovement to 83.59% for prepared premovement (p < 0.05). Along with the 4.67% improvement in classification accuracy, the standard deviation decreased by 0.95. Significance. The research findings confirm that incorporating a preparatory state into premovement enhances neural representations related to movement. This encoding enhancement paradigm effectively improves the performance of motor-based BCI. Additionally, this concept has the potential to broaden the range of decodable movement intentions and related information in motor-related BCI.
Effect of electron and ion mobility on edge biasing in tokamak plasmas
Authors: Shankar Vijay , Bisai N. , Raj Shrish , Sen A.
Published: May 2024

We present an improved model for the study of edge biasing in a tokamak plasma that incorporates electron and ion mobility contributions. The non-ambipolar nature of the drifts due to the electron/ion mobility terms influences the space charge separation due to edge biasing and affects plasma dynamics in the edge and SOL regions in a significant manner. In contrast to earlier studies, the present model enables simulation studies at higher biasing voltages. The inclusion of mobility enhances/decreases the effect of negative/positive biasing. The radial profiles of plasma density, electron temperature, radial electric field, and its shear for positive as well as negative biasing are investigated as a function of mobility.
Weak (non)conservation and stochastic dynamics of angular momentum
Authors: Matevosyan Ashot
Published: May 2024

Angular momentum conservation influences equilibrium statistical mechanics, leading to a generalized microcanonical density for an isolated system and a generalized Gibbs density for a weakly coupled system. We study the stochastic decay of angular momentum due to the weakly imperfect rotational symmetry of the external potential that confines the isolated many-particle system. We present a mesoscopic description of the system, deriving Langevin and Fokker–Planck equations, which are consistent with equilibrium statistical mechanics when rotational symmetry is maintained. When the symmetry is weakly violated, we formulate a coarse-grained stochastic differential equation governing the decay of total angular momentum over time. To validate our analytical predictions, we conduct numerical simulations of the microcanonical ensemble, an isolated system undergoing thermalization due to weak two-body interactions. Our coarse-grained Langevin equation accurately characterizes both the decay of the angular momentum and its fluctuations in a steady state. Furthermore, we estimate the parameters of our mesoscopic model directly from simulations, providing insights into the dissipative phenomenological coefficients, such as friction. More generally, this study contributes to a deeper understanding of the behavior of the integrals of motion when the corresponding symmetry is weakly violated.
Electric-magnetic duality and

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2

symmetry enriched Abelian lattice gauge theory
Authors: Jia Zhian , Kaszlikowski Dagomir , Tan Sheng
Published: May 2024

Kitaev’s quantum double model is a lattice realization of Dijkgraaf–Witten topological quantum field theory. Its topologically protected ground state space has broad applications for topological quantum computation and topological quantum memory. We investigate the

Z

2

symmetry enriched generalization of the model for the Abelian group in a categorical framework and present an explicit Hamiltonian construction. This model provides a lattice realization of the

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2

symmetry of the topological phase. We discuss in detail the categorical symmetry of the phase, for which the electric-magnetic (EM) duality symmetry is a special case. The aspects of symmetry defects are investigated using the G-crossed unitary braided fusion category. By determining the corresponding anyon condensation, the gapped boundaries and boundary-bulk duality are also investigated. In the last part, an explicit lattice realization of EM duality is discussed.
Directly electrospun copper ferrite CuFe2O4 nanofiber-based for gas classification
Authors: Phan Hong Phuoc , Nguyen Van Hoang , Nguyen Ngoc-Viet , Nguyen Van Hieu
Published: May 2024

The cross-response is a considerable primary challenge of gas sensors based on semiconducting metal oxide (SMO), especially in detecting and classifying gases with comparable properties. In this work, the copper ferrite (CuFe2O4, CFO) nanofibers (NFs)-based sensors were straightforwardly synthesised by electrospinning technique. The morphology of the CFO NFs was observed using scanning electron microscopy (SEM), which revealed a rough surface with a diameter of approximately 80 nm. The composition of the fiber was confirmed by energy dispersive spectroscopy (EDS), which showed the fiber’s chemical elements to include Cu, Fe, and O. The microstructural characteristics of the CFO NFs were analysed using x-ray diffraction (XRD) and Raman spectroscopy, confirming the characteristic peaks of the CFO phase. The gas sensing characteristics of CFO-based sensors have been examined to 25−200 ppm of various gases of (CH3)2CO, CH3CH2OH, NH3, and H2 at a function of working temperature of 350−450 °C. The gas-sensing mechanism of the sensor based on CFO NFs is explained by the surface depletion layer and the grain boundary model. The successful categorisation of these gases into distinct groups was realised, indicating that the issue of cross-response caused by interfering gases was effectively addressed with the aid of an artificial intelligence algorithm.
Facile one-step synthesis of in situ WO3@Gr nanorods as an efficient material for antimicrobial and decoloration applications
Authors: Nguyen Khoa Dang , Thinh Le Nguyen Quang , Tieu Linh Tieu Loan , Nguyen Thuy Huong , Anh Luu Thi Lan , Nguyen Huu Hung , Nguyen Cong Tu , Nguyen Ngoc Phuong Thao
Published: May 2024

This work examined the synthesis, antibacterial activity, and decolourisation of WO3@Graphene nanorods (WO3@Gr NR). WO3@Gr NR nanocomposite was in situ produced via a facile one-step hydrothermal process employing sodium tungstate dihydrate and exfoliated graphene as precursors. The resulted NR exhibited an average diameter of 13 nm, a large specific surface area of 53.3 m2 g−1, and a bimodal pore size distribution with an average pore size of 5.5 nm. The optical bandgap is extrapolated to be 2.75 eV. Graphene was shown to be responsible for the sample’s elaborate visible-light absorption, which improved adsorption and the ability to harvest visible light. WO3@Gr NR are more efficient against E. coli than S. aureus, killing up to 52% and 39% of cells, respectively, after two hours of treatment. When used in conjunction with invisible light, the NR killed E. coli and S. aureus by 78 and 62%, respectively. The bactericidal activity of photoinduced WO3@Gr NR was evaluated against P. aerugunosa, E. faecalis, E. coli, and S. aureus. The photocatalytic constant rates of organic dye methylene blue (MB) were determined to be 0.01 min−1. An IC50 (50% cell growth inhibition) value of 97 (μg ml−1) was determined for the nanocomposite against human liver cancer cell lines (HepG2). Our findings suggest that this nanorod may be utilised to degrade bacteria and organic colours in wastewater simultaneously while posing no risk to human health.
Indigenous, ethnic, and racial diversity and climate justice: New Zealand’s climate adaptation policies and policy approaches
Authors: Jayawardena Iresh
Published: May 2024

This research paper interrogates the extent to which indigenous, ethnic, and racial diversity is substantively integrated into climate justice discussions with a focus on New Zealand’s climate change adaptation policies. A qualitative research design is used, employing a documentary analysis and summative content analysis to scrutinise New Zealand climate change adaptation policies and their responsiveness to indigenous, ethnic and racial diversity within the ambit of climate justice. This study aims to measure the extent to which these policies promote inclusive and equitable climate adaptation outcomes. This study makes a significant contribution to the nuanced understanding of climate justice research, particularly regarding indigenous and ethnic minority communities. The study is expected to contribute to the existing knowledge base and inform the formulation of inclusive policies that integrate the diverse perspectives of these communities into climate adaptation and policy-making processes. The research findings highlight existing gaps and emphasise the importance of incorporating indigenous, ethnic, and racial diversity into policy development and implementation. The aim is to shape climate adaptation strategies that are representative of aware of insights from various communities in contemporary cities.
Book of Daniel
Authors: Portier-Young Anathea E.
Published: May 2024

Extant in three main ancient editions, the book of Daniel is a Jewish text composed c. 165 bce. Major themes are divine and human sovereignty, allegiance, identity, knowledge, and eschatology. The bilingual Hebrew and Aramaic version preserved in the Masoretic Text (MT) comprises twelve chapters and is one of the earliest examples of the apocalypse literary genre. Chapters 1–6 contain court legends about four Judean captives in Babylon—Daniel, Hananiah, Azariah, and Mishael (renamed Belteshazzzar, Shadrach, Meshach, and Abednego)—during the reigns of four kings: Nebuchadnezzar, Belshazzar, Darius, and Cyrus. Daniel excels as an interpreter of dreams and visions, yet as the four Judeans rise to positions of power, they must choose between loyalty to king and loyalty to God. Shadrach, Meshach, and Abednego are sentenced to death in a fiery furnace for refusing to worship an idol, and Daniel is thrown into a pit of lions for praying to his deity. Yet each of the four experiences divine deliverance. In chapters 7–12, Daniel recounts a series of apocalyptic visions and discourses foretelling a sequence of empires and the concomitant subjugation, suffering, resistance, and deliverance of the Judean people. The ancient Greek versions of the text, Old Greek and Proto-Theodotion, differ in various respects from MT Daniel, most notably in their inclusion of the tales of Susanna and Bel and the Dragon, the Prayer of Azariah, and the Song of the Three Youths. The book of Daniel influenced the development of Jewish and Christian eschatology, including beliefs about resurrection and judgment after death. Early Christian art and liturgy drew on the tales in Daniel to express hope of salvation. In the synoptic gospels, Jesus identifies himself with the “one like a human being” (commonly translated “son of man”; Dan. 7), implicitly identifying the kingdom he inaugurates with the kingdom of the holy ones that succeeds the four empires in Daniel’s vision.
Integrating randomized and observational studies to estimate optimal dynamic treatment regimes
Authors: Batorsky Anna , Anstrom Kevin J , Zeng Donglin
Published: May 2024

Sequential multiple assignment randomized trials (SMARTs) are the gold standard for estimating optimal dynamic treatment regimes (DTRs), but are costly and require a large sample size. We introduce the multi-stage augmented Q-learning estimator (MAQE) to improve efficiency of estimation of optimal DTRs by augmenting SMART data with observational data. Our motivating example comes from the Back Pain Consortium, where one of the overarching aims is to learn how to tailor treatments for chronic low back pain to individual patient phenotypes, knowledge which is lacking clinically. The Consortium-wide collaborative SMART and observational studies within the Consortium collect data on the same participant phenotypes, treatments, and outcomes at multiple time points, which can easily be integrated. Previously published single-stage augmentation methods for integration of trial and observational study (OS) data were adapted to estimate optimal DTRs from SMARTs using Q-learning. Simulation studies show the MAQE, which integrates phenotype, treatment, and outcome information from multiple studies over multiple time points, more accurately estimates the optimal DTR, and has a higher average value than a comparable Q-learning estimator without augmentation. We demonstrate this improvement is robust to a wide range of trial and OS sample sizes, addition of noise variables, and effect sizes.
Preparation of biomass carbon dots/carboxymethyl cellulose-based fluorescent hydrogel: combines selective detection and visual adsorption for Copper(II)
Authors: Liang Sijie , Feng Huixia , Chen Nali , Wang Bin , Hu Mengyu , Huang XiaoXue , Yang Kai , Gu Yiming
Published: May 2024

In this study, we used nitrogen-doped carbon dots (NCDs), which were synthesized via the hydrothermal method of corn-stover biomass as raw material and polyethyleneimine as the nitrogen source, introduced them into the carboxymethyl cellulose (CMC)-based hydrogel to prepare an environmentally friendly fluorescent cellulose-based hydrogel (NCDs/CMC-PAM). NCDs/CMC-PAM was also used for simultaneous fluorescence monitoring and removal of Cu (II) in aqueous solution. The chemical and physical structures, adsorption behaviors and fluorescent properties of NCDs/CMC-PAM were investigated. The results showed that NCDs/CMC-PAM exhibited a well-linear response range of fluorescence response for Cu (II) (0∼100 μM, detection limit of 3.42 μM). NCDs/CMC-PAM showed maximum adsorption capacities of 237.71 mg/g for Cu (II), the adsorption process followed the Langmuir isotherm model and pseudo-second-order kinetic model, which is an exothermic spontaneous reaction with an increase in entropy. It can still maintain 79.03% of the original adsorption capacity after six cycles (pH = 6). The adsorption mechanisms of NCDs/CMC-PAM for Cu (II) are intraparticle diffusion, electrostatic attraction, ion exchange, and ligand interaction. Hence, the present study provides a new green way to synthesize an adsorbent that can be applied for the adsorption and detection of heavy metal ions.
First draft reference genome and annotation of the alternative oil species Physaria fendleri
Authors: Johnston Christopher R , Horn Patrick J , Alonso Ana Paula
Published: May 2024

In the wake of increasing demand for renewable energy sources, plant-based sources including alternative oilseeds have come to the forefront of interest. Hydroxy fatty acids (HFAs), produced in a few oilseed species, are important chemical feed stocks for industrial applications. An integrated approach was taken to assemble the first draft genome of the alternative HFA producer Physaria fendleri (n = 6), an outcrossing species with high heterozygosity. Both de novo transcriptome assemblies and genome assemblies were produced with public and generated sequencing reads. Resulting intermediate assemblies were then scaffolded and patched with multiple data sources, followed by super-scaffolding onto a masked genome of Camelina laxa (n = 6). Despite a current lack of available resources for the physical mapping of genomic scaffolds of P. fendleri, topography of the genome with respect to repeat and gene content was preserved at the scaffold level and not significantly lost via super-scaffolding. Read representation, gene and genome completion statistics, and annotation results illustrated the creation of a functional draft genome and a tool for future research on alternative oil species.
Posttranscriptional regulation of the T-box gene midline via the 3′UTR in Drosophila is complex and cell- and tissue-dependent
Authors: Makhijani Kalpana , Mar Jordan , Gaziova Ivana , Bhat Krishna Moorthi
Published: May 2024

The T-box (Tbx) proteins have a 180–230 amino acid DNA-binding domain, first reported in the Brachyury (T) protein. They are highly conserved among metazoans. They regulate a multitude of cellular functions in development and disease. Here, we report posttranscriptional and translational regulation of midline (mid), a Tbx member in Drosophila. We found that the 3′UTR of mid has mRNA degradation elements and AT-rich sequences. In Schneider S2 cells, mid-mRNA could be detected only when the transgene was without the 3′UTR. Similarly, the 3′UTR linked to the Renilla luciferase reporter significantly reduced the activity of the Luciferase, whereas deleting only the degradation elements from the 3′UTR resulted in reduced activity, but not as much. Overexpression of mid in MP2, an embryonic neuroblast, showed no significant difference in the levels of mid-mRNA between the 2 transgenes, with and without the 3′UTR, indicating the absence of posttranscriptional regulation of mid in MP2. Moreover, while elevated mid-RNA was detected in MP2 in nearly all hemisegments, only a fifth of those hemisegments had elevated levels of the protein. Overexpression of the 2 transgenes resulted in MP2-lineage defects at about the same frequency. These results indicate a translational/posttranslational regulation of mid in MP2. The regulation of ectopically expressed mid in the wing imaginal disc was complex. In the wing disc, where mid is not expressed, the ectopic expression of the transgene lacking the 3′UTR had a higher level of mid-RNA and the protein had a stronger phenotypic effect. These results indicate that the 3′UTR can subject mid-mRNA to degradation in a cell- and tissue-specific manner. We further report a balancer-mediated transgenerational modifier effect on the expression and gain of function effects of the 2 transgenes.
Towards a Broader Approach to Competition and the Environment: Market Power and Environmental Disasters
Authors: Filho Calixto Salomão , Pinto Ido Vitor Henrique , Sadami Arthur
Published: May 2024

This article explores the intersection between market power and the environment, based on a study of environmental disasters in Brazil and their relationship with the activities of dominant firms. It argues that a narrow focus on price dimensions of corporate behaviour limits the legal responses for addressing broader environmental concerns emerging from market power. This highlights the need for a broader approach to understanding the operation of major players and the resulting impact on the environment. The paper concludes by discussing the institutional implications of an integrated approach for diverse fields of law for addressing market power as a driver of environmental harm, emphasising the importance of structural remedies that transcend mere compensation of affected parties.
Buffered Lugol's Iodine Preserves DNA Fragment Lengths
Authors: Gignac P M , Valdez D , Morhardt A C , Lynch L M
Published: May 2024

Synopsis

Museum collections play a pivotal role in the advancement of biological science by preserving phenotypic and genotypic history and variation. Recently, contrast-enhanced X-ray computed tomography (CT) has aided these advances by allowing improved visualization of internal soft tissues. However, vouchered specimens could be at risk if staining techniques are destructive. For instance, the pH of unbuffered Lugol's iodine (I2KI) may be low enough to damage deoxyribonucleic acid (DNA). The extent of this risk is unknown due to a lack of rigorous evaluation of DNA quality between control and experimental samples. Here, we used formalin-fixed mice to document DNA concentrations and fragment lengths in nonstained, ethanol-preserved controls and 3 iodine-based staining preparations: (1) 1.25% weight-by-volume (wt/vol.) alcoholic iodine (I2E); (2) 3.75% wt/vol. I2KI; and (3) 3.75% wt/vol. buffered I2KI. We tested a null hypothesis of no significant difference in DNA concentrations and fragment lengths between control and treatment samples. We found that DNA concentration decreases because of staining—potentially an effect of measuring intact double-stranded DNA only. Fragment lengths, however, were significantly higher for buffered I2KI and control samples, which were not, themselves, significantly different. Our results implicate buffered I2KI as the appropriate choice for contrast-enhanced CT imaging of museum wet collections to safely maximize their potential for understanding genetic and phenotypic diversity.
Relative impacts of Varroa destructor (Mesostigmata:Varroidae) infestation and pesticide exposure on honey bee colony health and survival in a high-intensity corn and soybean producing region in northern Iowa
Authors: Rinkevich Frank D , Danka Robert G , Rinderer Thomas E , Margotta Joseph W , Bartlett Lewis J , Healy Kristen B
Published: May 2024

The negative effects of Varroa and pesticides on colony health and survival are among the most important concerns to beekeepers. To compare the relative contribution of Varroa, pesticides, and interactions between them on honey bee colony performance and survival, a 2-year longitudinal study was performed in corn and soybean growing areas of Iowa. Varroa infestation and pesticide content in stored pollen were measured from 3 apiaries across a gradient of corn and soybean production areas and compared to measurements of colony health and survival. Colonies were not treated for Varroa the first year, but were treated the second year, leading to reduced Varroa infestation that was associated with larger honey bee populations, increased honey production, and higher colony survival. Pesticide detections were highest in areas with high-intensity corn and soybean production treated with conventional methods. Pesticide detections were positively associated with honey bee population size in May 2015 in the intermediate conventional (IC) and intermediate organic (IO) apiaries. Varroa populations across all apiaries in October 2015 were negatively correlated with miticide and chlorpyrifos detections. Miticide detections across all apiaries and neonicotinoid detections in the IC apiary in May 2015 were higher in colonies that survived. In July 2015, colony survival was positively associated with total pesticide detections in all apiaries and chlorpyrifos exposure in the IC and high conventional (HC) apiaries. This research suggests that Varroa are a major cause of reduced colony performance and increased colony losses, and honey bees are resilient upon low to moderate pesticide detections.
Breviscapine ameliorates autophagy by activating the JAK2/STAT5/BCL2 pathway in a transient cerebral ischemia rat model
Authors: Cun Yongdan , Guo Cunxiao , Jin Yaju , Zhou Li , Zhang Chengcai , Chen Na , Peng Yicheng , Zhang Pengyue , Guo Yiting
Published: May 2024

Breviscapine (Bre), an extract from Erigeron breviscapus, has been widely used to treat cerebral ischemia but the mechanisms of its neuroprotective effects need to be clarified. The present study investigated whether Bre could alleviate excessive autophagy induced by cerebral ischemia in the rat middle cerebral artery occlusion (MCAO) ischemia model via activating the Janus kinase 2 (JAK2)/signal transducer and activator of transcription 5 (STAT5)/B-cell lymphoma 2 (BCL2) pathway. Rats were randomly divided into 5 groups, i.e. Sham group, MCAO+saline group, MCAO+Bre group, MCAO+DMSO (Dimethyl sulfoxide) group, and MCAO+Bre+AG490 (Tyrphostin AG490, the inhibitor of STAT5) group. The model was established and neuroprotection was evaluated by determining infarct volumes and conducting neurological behavioral tests. Autophagy levels in the infarct penumbra were detected using transmission electron microscopy and Western blotting. The expression of proteins in the JAK2/STAT5/BCL2 pathway was tested by Western blotting. Compared to the MCAO+saline group, the infarct volumes in the MCAO+Bre group were significantly reduced and neurological behavior improved. Breviscapine administration also significantly increased p-JAK2, p-STAT5, and BCL2 expression but decreased autolysosome numbers; it also downregulated Beclin-1 expression and the LC3II/LCI ratio. The JAK2 inhibitor AG490 reversed these effects. These findings indicate that breviscapine can improve neural recovery following ischemia through alleviating excessive autophagy and activation of the JAK2/STAT5/BCL2 axis.
The ‘inherent vulnerability’ of women on the move: A gendered analysis of Morocco’s migration reform
Authors: Norman Kelsey P , Reiling Carrie
Published: May 2024

Beginning in the 1990s, Morocco increasingly became a de facto host country for sub-Saharan migrants and asylum seekers originally intending to reach Europe. While the government’s treatment toward these groups was characterized by informality and violence throughout the early 2000s, Morocco embarked on a reform process in 2013 that included a regularization process for irregular migrants. During the regularization process, the Moroccan government automatically granted all women applicants residency status due to their presumed ‘vulnerability’. This paper asks: What are the implications of assuming that women are ‘inherently vulnerable’? Drawing on in-person interviews and an analysis of policy documents, this article adds to the gendered migration and refugee literature by demonstrating that supposedly humanitarian policies toward women can also victimize them, stereotype male migrants and refugees as threatening, and strengthen the patriarchal role of the state and its ability to carry out violence in the name of protection.
On the necessity of a pluralist theory of reparations for historical injustice
Authors: Lambrecht Felix
Published: May 2024

Philosophers have offered many arguments to explain why historical injustices require reparations. This paper raises an unnoticed challenge for almost all of them. Most theories of reparations attempt to meet two intuitions: (1) reparations are owed for a past wrong and (2) the content of reparations must reflect the historical injustice. I argue that necessarily no monistic theory can meet both intuitions. I do this by showing that any theory that can meet intuition (1) necessarily cannot also meet intuition (2). This result suggests that a theory of reparations must either sacrifice one of the two intuitions or be pluralist. I argue that we ought to prefer the pluralist theory over the monistic theory. I sketch the pluralist theory, and I defend it by considering an objection about the way it can resolve conflicts.
Brain-wide representation of social knowledge
Authors: Alcalá-López Daniel , Mei Ning , Margolles Pedro , Soto David
Published: May 2024

Understanding how the human brain maps different dimensions of social conceptualizations remains a key unresolved issue. We performed a functional magnetic resonance imaging (MRI) study in which participants were exposed to audio definitions of personality traits and asked to simulate experiences associated with the concepts. Half of the concepts were affective (e.g. empathetic), and the other half were non-affective (e.g. intelligent). Orthogonally, half of the concepts were highly likable (e.g. sincere) and half were socially undesirable (e.g. liar). Behaviourally, we observed that the dimension of social desirability reflected the participant’s subjective ratings better than affect. FMRI decoding results showed that both social desirability and affect could be decoded in local patterns of activity through distributed brain regions including the superior temporal, inferior frontal, precuneus and key nodes of the default mode network in posterior/anterior cingulate and ventromedial prefrontal cortex. Decoding accuracy was better for social desirability than affect. A representational similarity analysis further demonstrated that a deep language model significantly predicted brain activity associated with the concepts in bilateral regions of superior and anterior temporal lobes. The results demonstrate a brain-wide representation of social knowledge, involving default model network systems that support the multimodal simulation of social experience, with a further reliance on language-related preprocessing.
Two laterally based scrotal pedicled flap grafts in the treatment of penile skin necrosis due to ring incarceration: a case series
Authors: Xie Jiaokui
Published: May 2024

Introduction

The rise in the incidence of penile ring incarceration has led to additional cases of ischemic necrosis of the penile skin. Two laterally based scrotal pedicled flaps (LSPFs), noted for their rich blood flow and skin source, resemble penile skin and are the preferred donor sites for repairing such necrosis.

Aims

This study summarizes the outcomes of 2 LSPF grafts for the treatment of penile skin necrosis.

Methods

Data were collected from 5 patients with penile skin necrosis due to ring incarceration who sought treatment at Ankang Central Hospital between 2012 and 2023.

Results

All patients exhibited varying degrees of necrosis in the urethral corpus cavernosum and the penis’s anterior tip. Two LSPFs were used for wound repair, with direct suturing of the donor site. None of the 5 patients experienced flap necrosis postsurgery, and they regained normal urination function. The patients reported satisfaction with both the aesthetic and functional results.

Conclusion

Two LSPF grafts are an effective approach for repairing penile skin defects. They reliably cover necrotic penile skin defects, prevent further wound progression, preserve penile structure, and improve patients’ life quality.
Assessing Seed Treatments to Control Sudden Death Syndrome Caused by Fusarium virguliforme and Seedling and Root Disease Caused by Rhizoctonia sp. on Mungbean (Vigna radiata)
Authors: Batzer Jean C. , Wiggs Stith , Platner-Heidt Evelyn , Mueller Daren S.
Published: May 2024

There is growing interest in producing mungbean ( Vigna radiata L. Wilczek) in the United States, which is driven by increased consumer demand. Strategies are needed for United States farmers to take advantage of this high-value crop and its environmental sustainability. Recommendations for the management of mungbean seedling and root diseases are lacking. Preliminary research in central Iowa mungbean fields from 2019 to 2023 has shown that mungbean is particularly vulnerable to Fusarium virguliforme, the cause of soybean sudden death syndrome (SDS), and Rhizoctonia sp., the cause of damping-off, root decay, premature defoliation, and pod abortion. The purpose of this study was to screen a variety of fungicides as a seed treatment or a soil band application to control root rot in mungbean. We performed three field studies over 2 years using mungbean cultivars Berken and OK2000. Seed treatments Evergol Energy + fluopyram and Evergol Energy + pydiflumetofen showed the highest performance ( P < 0.05), with approximately 30% more healthy roots than nontreated controls. Other treatments exhibited about 20% more healthy roots than the nontreated control. Biotam in-furrow application showed the highest plant population for ‘OK2000’, but we observed no treatment differences in plant stand for ‘Berken’.
A New Approach in Management of Orbital Adherence Syndrome
Authors: Hasanov Farman , Davudov Mahammad , Isgandarova Surayya
Published: May 2024

Orbital walls are one of the most common sites of midface fractures and account for ~40% of traumatic injuries in this region. These fractures are often associated with changes in the anatomy of the orbital cavity and frequently affect the orbital inferior wall, infraorbital groove and canal, and medial orbital wall, which leads to changes in its pattern and volume as well. Generally, the forces required for brake superior and lateral walls are greater than those required for thin medial and inferior walls. Disruption of any of these structures leads to the expansion of orbital volume that brings to the appearance of enophthalmos, diplopia, and impaired ocular mobility. The gold standard in the treatment of orbital wall fractures is surgical reconstruction, that includes fracture site exposure, freeing tissue prolapsed into the fracture site, and re-approximating the orbital wall support, usually with an orbital implant. It usually could be achieved by the usage of such as transconjunctival, subciliary, and coronal approaches and implementation of graft and reconstructive materials, including bones, cartilage, titanium, and resorbable mesh. Today, the gold standard in orbital floor reconstruction is the application of titanium mesh orbital plates. However, their implementation could be associated with a number of postoperative complications, such as mispositioning and orbital adherence syndrome. Orbital adherence syndrome is a poorly described and understood phenomenon and appears to occur after the use of large-pored titanium mesh for orbital reconstruction. It usually appears as limited eye movement that appears 1 to 2 weeks after reconstructive procedure. Prevention is possible through careful patient selection and the placement of a smooth interface medium in the initial surgery. The aim of the current study is to present the outcomes of orbital reconstruction done by both orbital mesh and customized ​​smooth-surfaced titanium orbital implants.
Research progress of Chinese herbal medicines and classic prescriptions in the treatment of COPD based on the TCM theory and medicinal characteristics
Authors: Luo Qian , Peng Bo , Wei Xiaolu , Liu Yan , Li Wei , Liu Wei , Waqas Ahmed , Wang Caixia , Ye Zuguang , Zhang Guangping , Hou Hongping
Published: May 2024

Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease with a complex pathogenesis, which causes the lack of precise and personalized prevention, control, and treatment approaches in clinical practice. Traditional Chinese medicine (TCM) with multiple components acting on multiple targets plays a role in the prevention and treatment of COPD. After evaluating the treatment of cough, dyspnea, and lung distension based on syndrome differentiation in TCM, we summarized the commonly used TCM preparations for treating COPD. These preparations are mainly composed of medicines for clearing interior heat and releasing exterior, tonifying, activating blood and resolving stasis, resolving phlegm, relieving cough and breathlessness, and regulating Qi movement. Because all of them contain a variety of active ingredients such as flavonoids, terpenoids, and phenols, we analyzed the mechanisms of the classic prescriptions alone or in combination with other medicines or therapeutic methods. These mechanisms involve counteracting inflammation, oxidative stress, and fibrosis, inhibiting apoptosis, alleviating airway remodeling, and enhancing immunity. Meantime, we summarized the existing problems in the treatment of COPD by TCM. This review provides a scientific basis for the research and treatment of COPD in the future.
Acidithiobacillus acidisediminis sp. nov., an acidophilic sulphur-oxidizing chemolithotroph isolated from acid mine drainage sediment
Authors: Li Xiu-Tong , Liang Zong-Lin , Huang Ye , Jiang Zhen , Yang Zhen-Ni , Zhou Nan , Liu Ying , Liu Shuang-Jiang , Jiang Cheng-Ying
Published: May 2024

Strain S30A2T, isolated from the acid mine drainage sediment of Mengzi Copper Mine, Yunnan, is proposed to represent a novel species of the sulphur-oxidizing genus Acidithiobacillus. Cells were Gram-stain-negative, non-endospore forming, highly motile with one or two monopolar flagella and rod-shaped. The strain was mesophilic, growing at 30–50 °C (optimum, 38 °C), acidophilic, growing at pH 2.0–4.5 (optimum, pH 2.5), and tolerant of 0–4 % (w/v; 684 mol l−1) NaCl. The 16S rRNA gene-based sequence analysis showed that strain S30A2T belongs to the genus Acidithiobacillus and shows the largest similarity of 96.6 % to the type strain Acidithiobacillus caldus KUT. The genomic DNA G+C content of strain S30A2T was 59.25 mol%. The average nucleotide identity ANIb and ANIm values between strain S30A2T and A. caldus KUT were 70.95 and 89.78 %, respectively and the digital DNA–DNA hybridization value was 24.9 %. Strain S30A2T was strictly aerobic and could utilize elementary sulphur and tetrathionate to support chemolithotrophic growth. The major cellular fatty acid of S30A2T was C19 : 1ω7c. The respiratory quinones were ubiquinone-8 and ubiquinone-7. Based upon its phylogenetic, genetic, phenotypic, physiologic and chemotaxonomic characteristics, strain S30A2T is considered to represent a novel species of the genus Acidithiobacillus, for which the name Acidithiobacillus acidisediminis sp. nov. is proposed. The type strain is S30A2T (=CGMCC 1.17059T=KCTC 72580T).
Defining the heterogeneous molecular landscape of lung cancer cell responses to epigenetic inhibition
Authors: Lin Chuwei , Sniezek Catherine M. , McGann Christopher D. , Karki Rashmi , Giglio Ross M. , Garcia Benjamin A. , McFaline-Figeroa José L. , Schweppe Devin K.
Published: May 2024

Epigenetic inhibitors exhibit powerful antiproliferative and anticancer activities. However, cellular responses to small-molecule epigenetic inhibition are heterogenous and dependent on factors such as the genetic background, metabolic state, and on-/off-target engagement of individual small-molecule compounds. The molecular study of the extent of this heterogeneity often measures changes in a single cell line or using a small number of compounds. To more comprehensively profile the effects of small-molecule perturbations and their influence on these heterogeneous cellular responses, we present a molecular resource based on the quantification of chromatin, proteome, and transcriptome remodeling due to histone deacetylase inhibitors (HDACi) in non-isogenic cell lines. Through quantitative molecular profiling of 10,621 proteins, these data reveal coordinated molecular remodeling of HDACi treated cancer cells. HDACi-regulated proteins differ greatly across cell lines with consistent (JUN, MAP2K3, CDKN1A) and divergent (CCND3, ASF1B, BRD7) cell-state effectors. Together these data provide valuable insight into cell-type driven and heterogeneous responses that must be taken into consideration when monitoring molecular perturbations in culture models
Mechanical forces instruct division plane orientation of cambium stem cells during radial growth inArabidopsis thaliana
Authors: Höfler Mathias , Liu Xiaomin , Greb Thomas , Alim Karen
Published: May 2024

Precise regulation of cell division is central for the formation of complex multicellular organisms and a hallmark of stem cell activity. In plants, due to the absence of cell migration, correct placement of newly produced cell walls during cell division is of eminent importance for generating functional tissues and organs. In particular, during radial growth of plant shoots and roots, concerted cell divisions in the cambium are essential to produce adjacent xylem and phloem tissues in a strictly bidirectional manner. While several intercellular signaling cascades have been identified to instruct tissue organization during radial growth, a role of mechanical forces in guiding cambium stem cell activity has been frequently proposed but, so far, not been functionally investigated on the cellular level. Here, we coupled anatomical analyses with a cell-based vertex model to analyze the role of mechanical stress in radial plant growth at the cell and tissue scale. Simulations based on segmented cellular outlines of radially growingArabidopsishypocotyls revealed a distinct stress pattern with circumferential stresses in cambium stem cells which coincided with the orientation of cortical microtubules. Integrating stress patterns as a cue instructing cell division orientation was sufficient for the emergence of typical cambium-derived cell files and agreed with experimental results for stress-related tissue organization in confining mechanical environments. Our work thus underlines the significance of mechanical forces in tissue organization through self-emerging stress patterns during the growth of plant organs.
Distinct Tumor-TAM Interactions in IDH-Stratified Glioma Microenvironments unveiled by Single-Cell and Spatial Transcriptomics
Authors: Motevasseli Meysam , Darvishi Maryam , Khoshnevisan Alireza , Zeinalizadeh Mehdi , Saffar Hiva , Bayat Shiva , Najafi Ali , Abbaspour Mohammad Javad , Mamivand Ali , Olson Susan B. , Tabrizi Mina
Published: May 2024

Tumor-associated macrophages (TAMs) residing in the tumor microenvironment (TME) are characterized by their pivotal roles in tumor progression, antitumor immunity, and TME remodeling. However, a thorough comparative characterization of tumor-TAM crosstalk across IDH-defined categories of glioma remains elusive. We delineated the phenotypic heterogeneity of TAMs across IDH-stratified gliomas. Notably, two TAM subsets with a mesenchymal phenotype were enriched in IDH-WT glioblastoma (GBM) and correlated with poorer patient survival and reduced response to anti-PD1 immune checkpoint inhibitor (ICI). We proposed SLAMF9 receptor as a potential therapeutic target. Inference of gene regulatory networks identified PPARG, ELK1, and MXI1 as master transcription factors of mesenchymal BMD-TAMs. Analyses of reciprocal tumor-TAM interactions, revealed distinct crosstalk in IDH-WT tumors, including ANXA1-FPR1/3, FN1-ITGAVB1, VEGFA-NRP1, and TNFSF12-TNFRSF12A. Furthermore, we demonstrated significant upregulation ofANXA1, FN1, NRP1, andTNFRSF12Agenes in IDH-WT tumors using bulk RNA-seq and RT-qPCR. Longitudinal expression analysis of candidate genes revealed no difference between primary and recurrent tumors. Collectively, our study offers insights into the unique cellular composition and communication of TAMs in glioma TME, revealing novel vulnerabilities for therapeutic interventions in IDH-WT GBM.
Mitochondrial DNA is a sensitive surrogate and oxidative stress target in oral cancer cells
Authors: Tan Jingyu , Dong Xinlin , Liu Haiwen
Published: May 2024

Cellular oxidative stress mediated by intrinsic and/or extrinsic reactive oxygen species (ROS) is associated with disease pathogenesis. Oxidative DNA damage can naturally be substituted by mitochondrial DNA (mtDNA), leading to base lesion/strand break formation, copy number changes, and mutations. In this study, we devised a single test for the sensitive quantification of acute mtDNA damage, repair, and copy number changes using supercoiling-sensitive quantitative PCR (ss-qPCR) and examined how oxidative stress-related mtDNA damage responses occur in oral cancer cells. We observed that exogenous hydrogen peroxide (H2O2) induced dynamic mtDNA damage responses, as reflected by early structural DNA damage, followed by DNA repair if damage did not exceed a particular threshold. However, high oxidative stress levels induced persistent mtDNA damage and caused a 5–30-fold depletion in mtDNA copy numbers over late responses. This dramatic depletion was associated with significant growth arrest and apoptosis, suggesting persistent functional consequences. Moreover, oral cancer cells responded differentially to oxidative injury when compared with normal cells, and different ROS species triggered different biological consequences under stress conditions. In conclusion, we developed a new method for the sensitive detection of mtDNA damage and copy number changes, with exogenous H2O2inducing dynamic mtDNA damage responses associated with functional changes in stressed cancer cells. Finally, our method can help characterize oxidative DNA damage in cancer and other human diseases.
Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests
Authors: Hübner Lukas , Stamatakis Alexandros
Published: May 2024

The field of population genetics attempts to advance our understanding of evolutionary processes. It has applications, for example, in medical research, wildlife conservation, and – in conjunction with recent advances in ancient DNA sequencing technology – studying human migration patterns over the past few thousand years. The basic toolbox of population genetics includes genealogical tress, which describe the shared evolutionary history among individuals of the same species. They are calculated on the basis of genetic variations. However, in recombining organisms, a single tree is insufficient to describe the evolutionary history of the whole genome. Instead, a collection of correlated trees can be used, where each describes the evolutionary history of a consecutive region of the genome. The current corresponding state of-the-art data structure, tree sequences, compresses these genealogical trees via edit operations when moving from one tree to the next along the genome instead of storing the full, often redundant, description for each tree. We propose a new data structure, genealogical forests, which compresses the set of genealogical trees into a DAG. In this DAG identical subtrees that are shared across the input trees are encoded only once, thereby allowing for straight-forward memoization of intermediate results. Additionally, we provide a C++ implementation of our proposed data structure, calledgfkit, which is 2.1 to 11.2 (median 4.0) times faster than the state-of-the-art tool on empirical and simulated datasets at computing important population genetics statistics such as the Allele Frequency Spectrum, Patterson’sf, the Fixation Index, Tajima’sD, pairwise Lowest Common Ancestors, and others. On Lowest Common Ancestor queries with more than two samples as input,gfkitscales asymptotically better than the state-of-the-art, and is thus up to 990 times faster. In conclusion, our proposed data structure compresses genealogical trees by storing shared subtrees only once, thereby enabling straight-forward memoization of intermediate results, yielding a substantial runtime reduction and a potentially more intuitive data representation over the state-of-the-art. Our improvements will boost the development of novel analyses and models in the field of population genetics and increases scalability to ever-growing genomic datasets.

2012 ACM Subject Classification

Applied computing → Computational genomics; Applied computing → Molecular sequence analysis; Applied computing → Bioinformatics; Applied computing → Population genetics