bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonlinear evolution of weakly coupled double tearing modes with equilibrium sheared toroidal flow
Authors: Ying Y. Y. , Wang Z. M. , Zhang Y. Y. , Zhang W. , Meng X. D. , Ma Z. W. 
Published: October 2024

Abstract
The nonlinear evolution of weakly coupled double tearing modes (DTMs) with and without sheared toroidal flow is systematically investigated with the three-dimensional, toroidal-geometry, and nonlinear magneto-hydro-dynamics code CLT. Due to the explosive growth of the weakly coupled DTMs, the pressure crashes are much more severe than those caused by the strongly coupled DTMs. The weakly coupled DTMs can easily be decoupled by sheared toroidal flow, and then the mutually driven term between the two tearing modes becomes periodically positive and negative, leading to periodic growth. The interaction slows the rotation between the two tearing modes when the phase difference is close to 180°. When the islands are sufficiently large, the interaction can overcome the decoupling effect of the shear flow, and the two tearing modes then lock with each other. Due to the different coupling effects of the two tearing modes, the threshold island width or perturbed magnetic field for mode-locking increases with increasing separation. The coupling effect between the two tearing modes is also related to the resistivity. If the resistivity is high, the coupling effect between the two tearing modes can be huge. A stronger shear flow is needed to decouple them, and even a small island can lead to mode-locking in high-resistivity plasma.
Dispersive vacuum as a decoherence amplifier of an Unruh–DeWitt detector
Authors: Barros Pedro H M , Costa Helder A S 
Published: October 2024

Abstract
Recently, interest has been growing in studies on discrete or ‘pixelated’ space-time that, through modifications in the dispersion relation, can treat the vacuum as a dispersive medium. Discrete spacetime considers that spacetime has a cellular structure on the order of the Planck length, and if this is true we should certainly have observable effects. In this paper, we investigated the effects caused by the dispersive vacuum on the decoherence process of an Unruh–DeWitt detector, our setup consists of a uniformly accelerated detector, initially in a qubit state, which interacts with a massless scalar field during a time interval finite. We use dispersion relations drawn from doubly special relativity and Hořava–Lifshitz gravity, with these modifications the vacuum becomes dispersive and has a corresponding refractive index. We calculate the probability transition rates, the probability of finding the detector in the ground state, and the quantum coherence variation. Our results indicate that the decoherence process occurs more quickly in cases with changes in the dispersion relation in the regime of high accelerations and interaction time. Additionally, the decoherence increases as the vacuum becomes more dispersive due to the increase in the order of modification in the dispersion relation, and this happens because the dispersive vacuum amplifies the effects of quantum fluctuations that are captured by the detector when interacting with the field.
MicroLEDs for optical neuromorphic computing—application potential and present challenges
Authors: Kraneis R , Müller M , Higgins-Wood S , Kaelin N , Wehmann H-N , von Malm N , Werner C , Waag A 
Published: October 2024

Abstract
The slow non-radiative surface recombination velocity of gallium nitride (GaN) in combination with its highly efficient radiative recombination makes this material ideally suited for microLEDs with dimensions as small as 1 µm and even below, serving as the fundamental building block of micro-displays. However, due to their superior miniaturization potential and energy efficiency, GaN-based microLEDs have applications that extend well beyond display technology. Their capability to produce optical patterns with high resolution, which can be modulated at extremely high frequencies, makes them suitable for numerous other applications. We suggest exploiting these exciting properties for a new and potentially equally significant application: utilizing microLEDs in optical processing units for artificial intelligence workloads. In neuromorphic computing, relevant aspects of biological neural networks are emulated directly with either electronic circuits or photonic devices, avoiding the shortcomings of conventional digital computer technology for AI workloads, which generally require massively parallel information processing. GaN microLEDs are discussed here as a promising enabling technology for optical neuromorphic processing units. We see great potential to substantially decrease power consumption through massively parallel in-memory processing combined with efficient photon production and detection. A theoretical analysis of scalability and energy efficiency is provided. A macroscopic bench-top optical microLED demonstrator is presented, which experimentally proves the feasibility of our approach. Future potential and challenges associated with miniaturizing and scaling microLED-based optical processing units are discussed. Finally, we summarize the open research questions that require attention before fully functional and miniaturized optical neuromorphic processing units based on GaN microLEDs can be realized.
Improvement of optical noise in optical-injection-locked quantum dot lasers epitaxially grown on silicon by reducing external carrier noise
Authors: Qu Luochen , Chu Qi , Wang Wenlu , Jin Zhiyong , Ding Shihao , Wang Cheng , Xu Xiaochuan , Wang Jiawei , Duan Jianan 
Published: October 2024

Abstract
This study theoretically investigates the impact of external carrier noise from pumping sources on the optical noise of epitaxial quantum dot (QD) lasers on silicon. The findings indicate that the spectral linewidth and relative intensity noise (RIN) of silicon-based QD lasers using a quiet pump are significantly reduced. At 5.5 times the threshold current, the spectral linewidth decreases from 337.2 kHz to 213.2 kHz, and the RIN decreases from −141.3 dB Hz−1 to −168.8 dB Hz−1. This reduction is attributed to the lower external carrier noise level of the quiet pump, which also suppresses the spectral linewidth rebroadening effect at a high bias current. Moreover, when external optical injection locking is applied, the spectral linewidth further decreases to 24 kHz at an injection ratio of −70 dB and to 1.8 mHz at 0 dB. The RIN also slightly decreases to −172.4 dB Hz−1 with an injection ratio of 10. These results demonstrate that using a quiet pump is an effective and manageable strategy for significantly reducing both the spectral linewidth and RIN of QD lasers, thereby facilitating their application in next-generation photonic integrated circuits, continuous-variable quantum key distribution, quantum computing and ultra-precise quantum sensing.
Diffusion of adzuki bean (Vigna angularis) oligomeric polyphenols from seed coats to cotyledons during boiling
Authors: Aoyama Yutaka , Masuda Kaoru , Mitsui Satoko , Yokoi Takuya 
Published: October 2024

Abstract
Adzuki beans (Vigna angularis) are major legumes in East Asia, commonly used in traditional Japanese confections in the form of a paste. Although various types of polyphenols are present in seed coats, there are no reports on the diffusion of polyphenols to cotyledons during boiling. This study revealed that oligomeric polyphenols—such as dimeric and more proanthocyanidins—diffused more easily from seed coats to cotyledons than monomeric polyphenols—such as (+)-catechin and (−)-epicatechin—during heating. Microscopy suggested that diffusing polyphenols were bound to cotyledon proteins. Furthermore, bound polyphenols, poorly extracted by ethanol and acetone, contributed to the 1,1- diphenyl-2-picrylhydrazyl radical-scavenging activity of cooked cotyledons. Thus, smooth adzuki bean paste, made by boiling adzuki beans and removing the seed coats, contains oligomeric polyphenols that contribute to its antioxidant activity. By clarifying further physiological activities of polyphenols diffused through cotyledons, adzuki bean paste can be a potential functional ingredient.
Comprehensive mutational profiling identifies new driver events in cutaneous leiomyosarcoma
Authors: van der Weyden Louise , Del Castillo Velasco-Herrera Martin , Cheema Saamin , Wong Kim , Boccacino Jacqueline M , Offord Victoria , Droop Alastair , Jones David R A , Vermes Ian , Anderson Elizabeth , Hardy Claire , de Saint Aubain Nicolas , Ferguson Peter M , Clarke Emily L , Merchant William , Mogler Carolin , Frew Derek , Harms Paul W , Monteagudo Carlos , Billings Steven D , Arends Mark J , Ferreira Ingrid , Brenn Thomas , Adams David J 
Published: October 2024

Abstract

Background
Cutaneous leiomyosarcoma (cLMS) is a rare soft-tissue neoplasm, showing smooth muscle differentiation, that arises from the mesenchymal cells of the dermis. To date, genetic investigation of these tumours has involved studies with small sample sizes and limited analyses that identified recurrent somatic mutations in RB1 and TP53, copy number gain of MYOCD and IGF1R, and copy number loss of PTEN.

Objectives
To better understand the molecular pathogenesis of cLMS, we comprehensively explored the mutational landscape of these rare tumours to identify candidate driver events.

Methods
In this retrospective, multi-institutional study, we performed whole-exome sequencing and RNA sequencing in 38 cases of cLMS.

Results
TP53 and RB1 were identified as significantly mutated and thus represent validated driver genes of cLMS. COSMIC mutational signatures SBS7a/b and DBS1 were recurrent; thus, ultraviolet light exposure may be an aetiological factor driving cLMS. Analysis of significantly recurrent somatic copy number alterations, which represent candidate driver events, found focal (&lt; 10 Mb) deletions encompassing TP53 and KDM6B, and amplifications encompassing ZMYM2, MYOCD, MAP2K4 and NCOR1. A larger (24 Mb) recurrent deletion encompassing CYLD was also identified as significant. Significantly recurrent broad copy number alterations, involving at least half of a chromosome arm, included deletions of 6p/q, 10p/q, 11q, 12q, 13q and 16p/q, and amplification of 15q. Notably PTEN is located on 10q, RB1 on 13q and IGFR1 on 15q. Fusion gene analysis identified recurrent CRTC1/CRTC3::MAML2 fusions, as well as many novel fusions in individual samples.

Conclusions
Our analysis of the largest number of cases of cLMS to date highlights the importance of large cohort sizes and exploration beyond small targeted gene panels when performing molecular analyses, as it allowed a comprehensive exploration of the mutational landscape of these tumours and identification of novel candidate driver events. It also uniquely afforded the opportunity to compare the molecular phenotype of cLMS with LMS of other tissue types, such as uterine and soft-tissue LMS. Given that molecular profiling has resulted in the development of novel targeted treatment approaches for uterine and soft-tissue LMS, our study now allows the same opportunities to become available for patients with cLMS.
Does pollination by non-flying mammals contribute substantially to fruit set of Banksia (Proteaceae)? A test in four species with contrasting floral traits
Authors: Wawrzyczek Stanislaw K , Davis Robert A , Krauss Siegfried L , Hoebee Susan E , Phillips Ryan D 
Published: October 2024

Abstract
Pollination by non-flying mammals (NFMs) is thought to be associated with cryptic, dull coloured, strongly scented flowers. In Western Australia, various Banksia species exhibit these traits, suggesting adaptation to primary pollination by NFMs, particularly the marsupial honey possum (Tarsipes rostratus). Here, we compare floral visitation rates and assess contribution to fruit set of NFMs and other pollinators in four species of Banksia with contrasting floral traits. Camera trap-based surveys revealed that honeyeater birds visited all species equally and were more frequent visitors than NFMs to the brightly coloured, unscented flowers of B. sessilis and B. splendida. By contrast, NFMs were more frequent visitors of the cryptic, strongly scented flowers of B. shuttleworthiana and B. subulata. Selective pollinator exclusion experiments showed that NFMs, birds, and insects contributed to pollination of all four species but indicated primary pollination by NFMs in B. subulata. Surprisingly, the most frequent visitors of this species were mice, not marsupials, providing the first compelling evidence of primary pollination by rodents in Australia. Notably, honey possums contributed substantially to fruit set of B. sessilis and B. splendida, despite infrequent visitation to these species. These findings challenge the assumption that in Banksia floral crypsis and strong scents are adaptations to primary pollination by honey possums. Instead, they suggest a spectrum of bird-NFM pollination systems, with rodents as key pollinators of some species.
Dysregulation of protein SUMOylation networks in Huntington’s disease R6/2 mouse striatum
Authors: Kachemov Marketta , Vaibhav Vineet , Smith Charlene , Sundararaman Niveda , Heath Marie , Pendlebury Devon F , Matlock Andrea , Lau Alice , Morozko Eva , Lim Ryan G , Reidling Jack , Steffan Joan S , Van Eyk Jennifer E , Thompson Leslie M 
Published: October 2024

Abstract
Huntington’s disease is a neurodegenerative disorder caused by an expanded CAG repeat mutation in the Huntingtin (HTT) gene. The mutation impacts neuronal protein homeostasis and cortical/striatal circuitry. SUMOylation is a post-translational modification with broad cellular effects including via modification of synaptic proteins.
Here, we used an optimized SUMO protein-enrichment and mass spectrometry method to identify the protein SUMOylation/SUMO interaction proteome in the context of Huntington’s disease using R6/2 transgenic and non-transgenic mice.
Significant changes in the enrichment of SUMOylated and SUMO-interacting proteins were observed, including those involved in presynaptic function, cytomatrix at the active zone, cytoskeleton organization and glutamatergic signalling. Mitochondrial and RNA-binding proteins also showed altered enrichment. Modified SUMO-associated pathways in Huntington’s disease tissue include clathrin-mediated endocytosis signalling, synaptogenesis signalling, synaptic long-term potentiation and SNARE signalling. To evaluate how modulation of SUMOylation might influence functional measures of neuronal activity in Huntington’s disease cells in vitro, we used primary neuronal cultures from R6/2 and non-transgenic mice. A receptor internalization assay for the metabotropic glutamate receptor 7 (mGLUR7), a SUMO-enriched protein in the mass spectrometry, showed decreased internalization in R6/2 neurons compared to non-transgenic neurons. SiRNA-mediated knockdown of the E3 SUMO ligase protein inhibitor of activated STAT1 (Pias1), which can SUMO modify mGLUR7, reduced this Huntington’s disease phenotype. In addition, microelectrode array analysis of primary neuronal cultures indicated early hyperactivity in Huntington’s disease cells, while later time points demonstrated deficits in several measurements of neuronal activity within cortical neurons. Huntington’s disease phenotypes were rescued at selected time points following knockdown of Pias1.
Collectively, our results provide a mouse brain SUMOome resource and show that significant alterations occur within the post-translational landscape of SUMO-protein interactions of synaptic proteins in Huntington’s disease mice, suggesting that targeting of synaptic SUMO networks may provide a proteostatic systems-based therapeutic approach for Huntington’s disease and other neurological disorders.
Gateway to the study of the amygdala and emotion
Authors: Romanski Lizabeth M 
Published: October 2024

Abstract
The study of the amygdala and its role in the processing of emotions has become a common focus in neuroscience. The modern expansion of research in this area is partly due to the discovery of a subcortical pathway for the transmission of emotional information and the experimental paradigm that was developed to study it. Groundbreaking experiments during the 90s utilized anatomical, neurophysiological, and behavioral lesion studies in a rodent animal model to uncover the neural circuitry of a simple emotional memory. These studies demonstrated the essential role of a specific monosynaptic pathway in emotional memory, using traditional tools and behavioral methods. The development of an animal model with a simple and appropriate classical conditioning paradigm made experimental investigations into the neural basis of emotion tenable and available to a generation of neuroscientists. These tools and a focus on the amygdala’s neural connections and their essential role in emotional memory were a driving force in the explosion of research regarding the amygdala and emotion.
Determination of Residual Dimethyl Sulfate in Cephalosporin Using HS-SPME/GC–MS
Authors: Lu Rongchun 
Published: October 2024

Abstract
Dimethyl sulfate (DMS) is widely used in manufacturing process but because of its genotoxicity nature, it should be monitored at trace levels (1 μg/mL). It is complicated and difficult to quantify DMS in cephalosporin with traditional method. Herein, a method for quantifying residual DMS in cephalosporin was developed, without complex sample preprocessing, no need for a large amount of solvent, employing headspace solid-phase microextraction (SPME) and gas chromatography–mass spectrometry (GC–MS). Compared with polydimethylsiloxane (PDMS)/divinylbenzene and polyacrylate fibers, PDMS was more suitable for absorbing DMS. The research showed that the PDMS fiber should be changed after 50 adsorption–desorption cycles. Linear regression analysis of the calibration curve demonstrated a robust linear relationship, with R2 of 0.999, across a concentration range of 0.25 to 4.0 μg/mL. The method underwent rigorous validation for specificity, linearity, precision and accuracy. This method was proven effective in measuring DMS in complex matrices. The limits of detection and quantification for this method is 0.05 and 0.25 μg/mL, respectively, which has room for improvement.
Primary Care Guidance for Providers Who Care for Persons With Human Immunodeficiency Virus: 2024 Update by the HIV Medicine Association of the Infectious Diseases Society of America
Authors: Horberg Michael , Thompson Melanie , Agwu Allison , Colasanti Jonathan , Haddad Marwan , Jain Mamta , McComsey Grace , Radix Asa , Rakhmanina Natella , Short William R , Singh Tulika , Tookes Hansel 
Published: October 2024

Abstract
Advances in antiretroviral therapy (ART) have made it possible for persons with human immunodeficiency virus (HIV) to have a lifespan that approaches that of people without HIV without progressing to AIDS or transmitting HIV to sexual partners or infants. There is, therefore, increasing emphasis on maintaining health throughout the lifespan. To receive optimal medical care and achieve desired outcomes, persons with HIV must be consistently engaged in care and able to access uninterrupted treatment, including ART. Comprehensive, evidence-based HIV primary care guidance is, therefore, more important than ever. Creating a patient-centered, stigma-free care environment is essential for care engagement. Barriers to care must be decreased at the societal, health system, clinic, and individual levels. As the population ages and noncommunicable diseases arise, providing comprehensive healthcare for persons with HIV becomes increasingly complex, including management of multiple comorbidities and the associated challenges of polypharmacy while also attending to HIV-specific health concerns. Clinicians must address issues specific to preventive health, including cancer screening, providing recommended vaccinations, and promoting sexual health, including sexually transmitted infection diagnosis, treatment, and prevention. Clinicians also must address issues for specific populations, including persons of childbearing potential during preconception and pregnancy, children, adolescents, and transgender and gender-diverse individuals. This guidance from an expert panel of the HIV Medicine Association of the Infectious Diseases Society of America updates the previous 2020 HIV Primary Care Guidance.
Peak expiratory flow predicts the occurrence of postoperative pneumonia after esophagectomy for esophageal cancer
Authors: Sawai Shota , Nakatani Eiji , Sato Shinsuke , Hawke Philip , Mochizuki Takuma , Nishida Masato , Ogiso Hiroshi , Watanabe Masaya 
Published: October 2024

Summary
Expiratory flow is an important factor in the achievement of airway clearance that is required to prevent postoperative pneumonia (POP). Although peak expiratory flow (PEF) has been shown to predict the occurrence of POP in lung cancer patients after lobectomy, its predictive power in relation to esophagectomy for esophageal cancer remains unknown. This study assesses PEF as a predictor of POP in patients with esophageal cancer undergoing radical esophagectomy.
We conducted a single-center, retrospective cohort study of patients who underwent radical esophagectomy with gastric tube reconstruction at our institution between January 2007 and December 2022. Preoperative pulmonary functions, including PEF, were assessed before surgery. Additionally, POP was diagnosed as a Clavien-Dindo classification of Grade II or higher. Survival and pneumonia incidence were compared using the Kaplan–Meier method. Logistic regression analysis was used to examine the relationship between these variables and POP.
The study included 513 patients, of which 441 were men. POP occurred in 86 patients (16.7%). When all patients were stratified by %PEF into two groups, the group with %PEF lower that 80% had significantly poorer prognosis and higher incidence of pneumonia. Multivariable logistic regression analysis indicated that %PEF (OR: 0.986, 95%CI: 0.974–0.999, P = 0.030), along with age, BMI, preoperative treatment, and recurrent laryngeal nerve palsy were independent protective factors against POP.
These results reveal that %PEF predicts the development of POP following esophagectomy for esophageal cancer.
Compiling a versatile toolbox for inducible gene expression in Methanosarcina mazei
Authors: Hüttermann Johanna , Schmitz Ruth 
Published: October 2024

Abstract
Methanosarcina mazei is a model organism, providing a platform to explore methanoarchaeal regulation mechanisms on the transcriptional and translational level. This study investigates and evaluates various molecular tools to allow inducible gene expression in M. mazei. (i) The TetR/TetO system was utilized to induce expression of a designed antisense RNA directed against sRNA154 allowing to increase transcripts of asRNA154 (500-fold), resulting in a significant decrease of sRNA154 levels (tetracycline-induced knockdown mutant). Strong reduction of sRNA154 was further confirmed in the knockdown mutant by up to 50-fold decreased transcript levels of the genes nifH, glnK1, and glnA1, the stability of which is increased by sRNA154. (ii) For translational regulation, an RNA thermometer was designed and first-ever utilized in an archaeon, inserted into the 5′-untranslated region of a reporter gene, which showed enhanced protein expression upon a temperature shift from 30°C to 40°C. (iii) The long 5′-UTR of a trimethylamine (TMA)-inducible polycistronic mRNA was evaluated and studied as a potential genetic tool for induced gene expression on the translational level. However, we discovered TMA-dependent regulation occurs most likely on the transcript level. (iv) A new selection marker (nourseothricin resistance) was established for M. mazei using the streptothricin acetyltransferase gene. Taken together, our findings provide a foundation for future exploration of genetic regulation and inducible gene expression in M. mazei and other methanoarchaea, advancing genetic studies in these organisms and enhancing their potential for biotechnology applications.