bluuebunny/crossref_metadata_2025 huggingface dataset:
Autocrine TGF-β1 drives tissue-specific differentiation and function of resident NK cells
Authors: Sparano Colin , Solís-Sayago Darío , Zangger Nathan Sébastien , Rindlisbacher Lukas , Van Hove Hannah , Vermeer Marijne , Westermann Frederike , Mussak Caroline , Rallo Elisa , Dergun Stanislav , Litscher Gioana , Xu Yishu , Bijnen Mitchell , Friedrich Christin , Greter Melanie , Juranić Lisnić Vanda , Becher Burkhard , Gasteiger Georg , Oxenius Annette , Tugues Sonia
Published: December 2024

Group 1 innate lymphoid cells (ILCs) encompass NK cells and ILC1s, which have non-redundant roles in host protection against pathogens and cancer. Despite their circulating nature, NK cells can establish residency in selected tissues during ontogeny, forming a distinct functional subset. The mechanisms that initiate, maintain, and regulate the conversion of NK cells into tissue-resident NK (trNK) cells are currently not well understood. Here, we identify autocrine transforming growth factor-β (TGF-β) as a cell-autonomous driver for NK cell tissue residency across multiple glandular tissues during development. Cell-intrinsic production of TGF-β was continuously required for the maintenance of trNK cells and synergized with Hobit to enhance cytotoxic function. Whereas autocrine TGF-β was redundant in tumors, our study revealed that NK cell–derived TGF-β allowed the expansion of cytotoxic trNK cells during local infection with murine cytomegalovirus (MCMV) and contributed to viral control in the salivary gland. Collectively, our findings reveal tissue-specific regulation of trNK cell differentiation and function by autocrine TGF-β1, which is relevant for antiviral immunity.
Manipulating ambient pressure superconductivity in metal borocarbides through hole doping
Authors: Tian Qing , Zhang Wei , Xia Weiyi , Liu Hanyu , Wang Caizhuang
Published: December 2024

A Ca2B4C4 ternary compound obtained by using a machine learning (ML) guided structure search is found to be metastable with a formation energy of only 18 meV atom−1 above the convex hull but exhibits only marginal superconducting transition temperature (T
c). By replacing Ca with Na, the electronic density of states at the Fermi level is significantly enhanced, increasing the predicted T
c to 21.9 K. Extending this hole-doping strategy to other Ca–B–C compounds, we found that while Na4B2C22 remains superconducting with a T
c of 4.0 K, Na substitution in Ca2B4C8 transforms it from a semiconductor to a superconductor with a T
c of 28.9 K. The flat σ bands, particularly from the 2p
x
and 2p
y
orbitals of carbon, and a Van Hove singularity at the Fermi level, play crucial roles in enhancing the superconductivity. This work introduces a new class of B–C-based superconductors and broadens the compositional space for high-temperature superconducting materials.
SKS-Net: skeleton-strengthening network for surface defect segmentation
Authors: Zuo Haiqiang , Zheng Yubo , Huang Qizhou , Wang Rongdi
Published: December 2024

Surface defect detection is an important task in industrial production. Although significant progress has been made in deep learning-based defect segmentation methods, the low contrast between defect and background and the shape and scale diversity of defects limit the models’ detection accuracy and generalization ability. Therefore, realizing the full automation of surface defect detection still faces many challenges. To overcome these problems, this paper proposes a skeleton-strengthening network called SKS-Net, which provides stable and excellent surface defect detection performance even at low contrast and multi-scale. SKS-Net designs a skeleton-strengthening convolutional module to capture multi-scale features efficiently. The convolution kernel of this convolution module is closer to the shape of the segmentation target, which significantly reduces irrelevant regions and improves the feature extraction capability of the convolution kernel. This convolution module can be directly embedded into existing network structures without adding additional computational overhead. In addition, we design a new feature channel fusion module to extract key information from features at different levels. To improve the training effect, we introduce a multi-scale auxiliary supervision mechanism. The proposed model is evaluated on four different publicly available surface defect datasets and compared with other state-of-the-art models. Results show that SKS-Net performs exceptionally well in terms of accuracy, achieving 66.72% mIoU on the KolektorSDD dataset. The code is publicly available at https://github.com/Wanglaoban3/SKS-Net.git.
Flexible solid-state supercapacitors based on biowaste-derived activated carbon and nanomaterials for enhanced performance
Authors: Koroglu Dilara , Bingol Haluk , Uralcan Betul
Published: December 2024

Supercapacitors are energy storage devices with long cycle life that can harvest and deliver high power. This makes them attractive for a broad range of applications including flexible and lightweight wearable consumer electronics. In this work, we fabricate flexible solid-state supercapacitors with improved capacitance and cycle life. We synthesize activated carbon (AC) from cabbage leaves as a low cost, biowaste-derived active electrode material. To improve mechanical flexibility and conductivity, we incorporate reduced graphene oxide sheets (RGO) and carbon quantum dots (CQDs) into the electrodes. We show that at the optimum AC/RGO/CQD composition, the capacitance of the solid-state supercapacitor is maximized while its scan rate dependence and bending stability are simultaneously improved. We envision that this approach offers significant potential for delivering efficient energy storage devices for consumer electronics.
Experiments of acoustic resonance and vibration mode of kotsuzumi using paper pipe, V-shape pendulum, and carbon paper
Authors: Tabaru Marie , Funakura Tomohisa , Matsutani Akihiro
Published: December 2024

Kotsuzumi is a membranophone used in the traditional Japanese performing art of Noh. So far, there are few studies about kotsuzumi. In this study, to reveal the component of kotsuzumi’s sound, we experimentally verified the acoustic characteristics of kotsuzumi. Acoustic physics experiments were conducted using paper pipes, clay, pendulum, and carbon paper. Loudspeaker and microphone were used to produce and record sound, respectively. First, the characteristics of the acoustic resonance inside the difference cavity shapes of the bodies were measured. Second, vibration modes of the membrane and the body were measured. Finally, a professional performer played kotsuzumi to verify the measured acoustic characteristics. We found that a sound around 200 Hz was due to (0,1) mode of the front membrane of kotsuzumi, a sound around 800 Hz was due to the characteristics of the body as a resonator, and a sound around 1580 Hz was due to the vibration of the kotsuzumi’s body itself.
Electromagnetic design and analysis of a bell-shaped superconducting magnet for head fMRI using a novel hybrid optimization method
Authors: Mei Yunhao , Shang Wangnan , Mo Lei , Qiu Bensheng , Zhang Qing
Published: December 2024

In task-state functional magnetic resonance imaging scans, it is often necessary for subjects to perform certain task actions, which is difficult to achieve in traditional whole-body MRI systems. In this study, a bell-shaped head magnetic resonance superconducting magnet was designed using a novel hybrid optimization method that combines linear programming, genetic algorithm, and nonlinear programming. This magnet design offers the following advantages: (1) the small and compact volume of the magnet structure allows for vertical placement of the system, enabling subjects to be in a sitting position during the scan. (2) The off-center diameter of spherical volume region expands the subject’s field of view. (3) Only the subject’s head is positioned inside the scanning system, freeing the subject’s torso to cooperate in performing various tasks. This paper provides a detailed description of the entire design process, conducts a comprehensive analysis of the electromagnetic performance and material mechanical properties of the designed magnet, and designs a passive quench protection system for the subsequent manufacturing of the magnet, with simulations and discussions on the magnet’s quenching process under the protection of this system.
Study on the mechanism and characteristics of pulsed corona discharge in water
Authors: Kang Zhongjian , Wang Chunbin , Shen Yichao , Yu Yingbo , Gao Chong
Published: December 2024

Plasma pulse is a safe and environmentally friendly unconventional technology for enhancing oil and gas production. However, during the pulsed discharge process, an abnormal discharge phenomenon often occurs, which severely affects the performance of the equipment and is referred to as corona discharge. This paper combines laboratory discharge test data to theoretically analyze and validate through COMSOL simulation the mechanism of corona discharge generation under the same electrode gap distance. A comparative analysis with arc discharge is also conducted to further examine its characteristics, and nonlinear regression analysis is used to study the impedance variation of the plasma channel during corona discharge. Results indicate that the decrease in switch breakdown voltage in the later stages of continuous discharge leads to the generation of corona discharge. The impedance of the plasma channel can be characterized by a time-varying resistance model based on a double exponential function. Finally, validation through theoretical calculations and Simulink simulations achieves a fitting rate of over 99%. The research provides significant guidance for further analysis of corona discharge and the development of suppression methods in plasma pulse technology, contributing to the optimization of the equipment and enhancing its operational performance.
The Halbach and alternating polarity linear magnets array are designed for microparticle separation, based on magnetophoresis
Authors: baghdadi shahriar , malekshahi mazdak rad
Published: December 2024

Particle separation using magnetophoresis requires an inhomogeneous magnetic field which affects the microparticle. The more changes in the magnetic field, the greater the magnetic force. The changes could exist in various ways. In this article, the change to produce a more intensive inhomogeneous magnetic field is generated by rotating the magnets to a specific degree. The analyses are done for three-state magnet arrays. For this purpose, a device is fabricated and the mentioned arrays are embedded in it. First, the results are simulated. The mathematical piecewise algorithm is used to validate the simulation. By examining the states in the fabricated device the experimental results are extracted. Overall, the results demonstrated that the Halbach and alternating polarity linear arrays (both 90, and 180 degrees) have better efficiency and throughput than the regular design array (without magnet rotating). The Halbach designs are illustrated with approximately the same results. However, in alternating polarity linear array, 180 degrees the particle capturing rate stood in a better place than the other design. 
Negative cumulative residual extropy under concomitants of generalized order statistics based on Cambanis bivariate family with applications
Authors: Husseiny I. A. , Ramadan Magdy Nagy Ahmed Nagy , Mansi Ahmed Hamdi
Published: December 2024

Thermodynamics, statistical mechanics, and quantum mechanics are the branches of physics that use entropy and extropy measures. It also seems to quantify the degree of signal uncertainty in information theory. Recently, extropy has been widely used in the literature as a measure of dispersion or uncertainty. Within generalized Farlie-Gumbel-Morgenstern families, the Cambanis bivariate family holds a prominent position as an efficient and adaptable extended family. Motivated by this, our work gives numerous characterizations of Cambanis copula based on order statistics (OSs). Also, we study the negative cumulative residual extropy and various measures of information associated with it for concomitants generalized OSs.Moreover, we study OSs and sequential OSs for each information measure in a computational study. This study offers a few beautiful symmetrical and asymmetric relationships that these information measures satisfy. Additionally, the empirical technique is applied to the Cambanis family to estimate every measure of negative extropy discussed in this work. As a final step, we have examined a bivariate real-world data set for illustrative purposes.
Optical analog to adiabatic passages in two coupled nonlinear waveguides by resonance-locked inverse engineering
Authors: Naim Nida , Deng Li , Niu Yueping , Gong Shangqing
Published: December 2024

We discuss in this paper the optical analog to rapid adiabatic passage (RAP) and two-state stimulated Raman adiabatic passage (STIRAP) in coupled waveguides with nonlinearity. With the increase of the power of light propagating in waveguides, the nonlinearity can significantly prevent the two adiabatic passages from being successfully simulated. Nevertheless, we find that the negative role of the nonlinearity can be avoided under the assistance of the method of resonance-locked inverse engineering. The method implies redesigning the longitudinally varying detuning of the propagation constants. We further point out that the variation of the detuning does not have to be exactly the same as what the method suggests. As long as the detuning has similar trend to what the method shows, the RAP and two-state STIRAP can still be realized in nonlinear waveguides. This makes the waveguide structure more simpler. Based on our study, the applications of two-state adiabatic passages in designing directional couplers and beam splitters are extended from linear to nonlinear waveguides.
Information transmission by random flow of gamma-photons: optimization of data-acquisition time
Authors: Zinnatullin A , Shakhmuratov R , Vagizov F
Published: December 2024

We transmit classical information in the form of Windows-1253 codes for text by modulating the intensity of a random flow of Mössbauer gamma-photons. It is shown that the time required for reliable decoding of information can be significantly reduced by averaging the number of gamma-photons detected in certain time windows. We find the optimal duration of this time experimentally. The proposed protocol allows reliable extraction of information from a very noisy signal.
Task-relevant stimulus design improves P300-based brain–computer interfaces
Authors: Kim Jongsu , Cho Yang Seok , Kim Sung-Phil
Published: December 2024

Objective. In the pursuit of refining P300-based brain–computer interfaces (BCIs), our research aims to propose a novel stimulus design focused on selective attention and task relevance to address the challenges of P300-based BCIs, including the necessity of repetitive stimulus presentations, accuracy improvement, user variability, and calibration demands. Approach. In the oddball task for P300-based BCIs, we develop a stimulus design involving task-relevant dynamic stimuli implemented as finger-tapping to enhance the elicitation and consistency of event-related potentials (ERPs). We further improve the performance of P300-based BCIs by optimizing ERP feature extraction and classification in offline analyses. Main results. With the proposed stimulus design, online P300-based BCIs in 37 healthy participants achieve an accuracy of 91.2% and an information transfer rate (ITR) of 28.37 bits/min with two stimulus repetitions. With optimized computational modeling in BCIs, our offline analyses reveal the possibility of single-trial execution, showcasing an accuracy of 91.7% and an ITR of 59.92 bits/min. Furthermore, our exploration into the feasibility of across-subject zero-calibration BCIs through offline analyses, where a BCI built on a dataset of 36 participants is directly applied to a left-out participant with no calibration, yields an accuracy of 94.23% and the ITR of 31.56 bits/min with two stimulus repetitions and the accuracy of 87.75% and the ITR of 52.61 bits/min with single-trial execution. When using the finger-tapping stimulus, the variability in performance among participants is the lowest, and a greater increase in performance is observed especially for those showing lower performance using the conventional color-changing stimulus. Significance. Using a novel task-relevant dynamic stimulus design, this study achieves one of the highest levels of P300-based BCI performance to date. This underscores the importance of coupling stimulus paradigms with computational methods for improving P300-based BCIs.
A method for dynamically adjusting the difficulty of rehabilitation training tasks driven by attention level
Authors: Chen Raojing , Lv Jian , Qiang Ligang , Liu Xiang
Published: December 2024

Objective. Enhancements in the rehabilitation of motor and cognitive functions are significantly attainable through proactive patient engagement. The difficulty of rehabilitation tasks and the environment in which they are conducted directly impact patient motivation. Consequently, this study introduces a dynamic difficulty adjustment method for rehabilitation training tasks based on attention levels, designed to adjust task difficulty in real-time and augment the focus of participants on their training tasks. Approach. Electroencephalography (EEG) signals from participants were harnessed to train an attention classification model, enabling the acquisition of real-time attention level signals. Task difficulty levels were adjusted based on the fluctuating attention levels. A cohort of 30 participants was engaged to evaluate: (1) the impact on engagement when attention levels are utilized as dynamic difficulty triggers; (2) the influence of various task environments on concentration. The experiment was assessed through EEG signals and questionnaire data, with frequency domain analysis conducted on EEG signals to calculate concentration values and statistical analysis performed on additional data. Main results. The findings reveal that within an identical virtual reality (VR) environment, leveraging attention levels as triggers for difficulty adjustment markedly improves participants’ task concentration. Compared to 2D environments, VR environments substantially enhance participants’ sense of immersion, interest, and flow state, albeit with increased physical exertion during training. The integration of VR and attention level feedback is deemed the most effective strategy. Significance. These exploratory insights indicate that the proposed method paves a novel path for boosting patient engagement in rehabilitation. Immersive rehabilitation training, driven by attention levels, promises a more effective and captivating patient experience. This study advances the field by offering data-driven, personalized rehabilitation approaches, potentially culminating in superior patient outcomes and enhanced quality of life.
Simultaneous encoding of speed, distance, and direction in discrete reaching: an EEG study
Authors: Srisrisawang Nitikorn , Müller-Putz Gernot R
Published: December 2024

Objective. The complicated processes of carrying out a hand reach are still far from fully understood. In order to further the understanding of the kinematics of hand movement, the simultaneous representation of speed, distance, and direction in the brain is explored. Approach. We utilized electroencephalography (EEG) signals and hand position recorded during a four-direction center-out reaching task with either quick or slow speed, near and far distance. Linear models were employed in two modes: decoding and encoding. First, to test the discriminability of speed, distance, and direction. Second, to find the contribution of the cortical sources via the source localization. Additionally, we compared the decoding accuracy when using features obtained from EEG signals and source-localized EEG signals based on the results from the encoding model. Main results. Speed, distance, and direction can be classified better than chance. The accuracy of the speed was also higher than the distance, indicating a stronger representation of the speed than the distance. The speed and distance showed similar significant sources in the central regions related to the movement initiation, while the direction indicated significant sources in the parieto-occipital regions related to the movement preparation. The combination of the features from EEG and source localized signals improved the classification. Significance. Directional and non-directional information are represented in two separate networks. The quick movement resulted in improvement in the direction classification. Our results enhance our understanding of hand movement in the brain and help us make informed decisions when designing an improved paradigm in the future.
Efficient evaluation of lattice Green’s functions
Authors: Zhugayevych Andriy
Published: December 2024

We develop and implement efficient algorithms for calculating lattice Green’s functions (LGFs) at any point and argument. This includes several approaches: recurrence relations in lattice coordinates, series at zero and infinity, and finite-precision uniform approximations. The methodology can be applied to any simple lattice, whereas program code is provided for triangular and hypercubic lattices. In particular, the obtained generic recurrence relations are applicable to any lattice with a root-free band dispersion. Except for lattices with a high coordination number, these relations allow LGF to be presented as a linear combination of d non-polynomial functions with polynomial coefficients, where d is the lattice dimension. The non-polynomial functions are solutions of d-order differential equation with polynomial coefficients which allows their series expansion at singularities to be performed. For series at infinity, we estimate the remainder, thus extending its use to the zero value of the argument. The remainder itself provides a good finite-precision estimate for the LGF. Finally, we derive a large-scale approximation that smoothly connects the lattice and the continuum Green’s functions. The provided open-source code allows for arbitrary-precision and symbolic computations of LGF.
Local exotic tori
Authors: Brendel Joé
Published: December 2024

For a broad class of symplectic manifolds of dimension at least six, we find the following new phenomenon: there exist local exotic Lagrangian tori.

More specifically, let

X
X

be a geometrically bounded symplectic manifold of dimension at least six. We show that every open subset of

X
X

contains infinitely many Lagrangian tori which are distinct up to symplectomorphisms of

X
X

while being Lagrangian isotopic and having the same classical invariants. The proof relies on a locality property of the displacement energy germ, which allows us to compute it in a Darboux chart.

Since these tori are not monotone, bubbling may occur and the count of Maslov index two

J
J

-holomorphic disks does not yield an invariant.
Gromov–Witten/Pandharipande–Thomas correspondence via conifold transitions
Authors: Lin Yinbang , Wang Sz-Sheng
Published: December 2024

Given a projective conifold transition of smooth projective threefolds from

X
X

to

Y
Y

, we show that if the Gromov–Witten/Pandharipande–Thomas descendent correspondence holds for the resolution

Y
Y

, then it also holds for the smoothing

X
X

with stationary descendent insertions. As applications, we show the correspondence in new cases, especially for Fano threefolds.
A novel computational model ITHCS for enhanced prognostic risk stratification in ESCC by correcting for intratumor heterogeneity
Authors: Lu Tong , Guo Wei , Guo Wei , Meng Wangyang , Han Tianyi , Guo Zizhen , Li Chengqiang , Gao Shugeng , Ye Youqiong , Li Hecheng
Published: December 2024

Intratumor heterogeneity significantly challenges the accuracy of existing prognostic models for esophageal squamous cell carcinoma (ESCC) by introducing biases related to the varied genetic and molecular landscapes within tumors. Traditional models, relying on single-sample, single-region bulk RNA sequencing, fall short of capturing the complexity of intratumor heterogeneity. To fill this gap, we developed a computational model for intratumor heterogeneity corrected signature (ITHCS) by employing both multiregion bulk and single-cell RNA sequencing to pinpoint genes that exhibit consistent expression patterns across different tumor regions but vary significantly among patients. Utilizing these genes, we applied multiple machine-learning algorithms for sophisticated feature selection and model construction. The ITHCS model significantly outperforms existing prognostic indicators in accuracy and generalizability, markedly reducing sampling biases caused by intratumor heterogeneity. This improvement is especially notable in the prognostic assessment of early-stage ESCC patients, where the model exhibits exceptional predictive power. Additionally, we found that the risk score based on ITHCS may be associated with epithelial-mesenchymal transition characteristics, indicating that high-risk patients may exhibit a diminished efficacy to immunotherapy.
Queer voices in computational biology: the first ISCB LGBTQI+ Symposium
Authors: Parra R Gonzalo , Wass Mark N , Munholland Seth , Wiper Mallory L , Kovats Diane , Pantano Lorena , Dunbrack Roland L
Published: December 2024

The first ISCB LGBTQI+ Symposium, held during Pride Month in 2024, marked a significant milestone for the International Society for Computational Biology (ISCB) community to promote diversity. This event aimed to provide a safe and supportive space for LGBTQI+ members of the society to share their experiences, address unique challenges in Bioinformatics and Computational Biology, and foster strategies for creating an equitable environment within ISCB. Through keynote presentations, short talks, and a roundtable discussion, participants explored topics such as minority stress, visibility, and the impact of role models. The symposium was rooted in a recognition of the historical and ongoing marginalization faced by LGBTQI+ individuals and sought to challenge systemic barriers while emphasizing the importance of community and representation. This article details the journey behind organizing the symposium, including overcoming the challenges of ensuring inclusivity and privacy, and highlights the profound impact of role models and collective action in advancing LGBTQI+ equity in science.
Genetic signature of demographic history explains the current sympatric distribution of sibling species of Craseomys (Rodentia: Arvicolinae)
Authors: Saitoh Takashi , Murakami Shota , de Guia Anna Pauline O , Ohnishi Naoki , Kawai Kuniko
Published: December 2024

Sequences of mitochondrial DNA were analysed in two vole species (Craseomys rex and Craseomys rufocanus), which are closely related based on phylogeny, morphology, and ecology. In Hokkaido, Japan, they occur sympatrically in forests, but Craseomys rufocanus also inhabits open fields. Capture records of 2532 specimens from 114 localities confirmed the widespread and fragmented distribution of Craseomys rufocanus and Craseomys rex and indicated that abundance of Craseomys rufocanus was 9.2–19.8 times higher than that of Craseomys rex. The phylogenetic tree illustrated four regional clades for Craseomys rex, but no distinct clades for Craseomys rufocanus. The observed mismatch distribution of Craseomys rufocanus matched with a spatial expansion model, indicating population expansion through range extension with frequent migration. Using 47 haplotypes from 151 Craseomys rex and 302 haplotypes from 1037 Craseomys rufocanus, a skyline plot revealed that Craseomys rufocanus increased during the Last Glacial Cycle (LGC) when grassy vegetation dominated forests. Craseomys rex expanded following forest recovery following LGC survival. The current effective population size (Ne) of Craseomys rufocanus was 15.9–33.8 times higher than that of Craseomys rex, in good agreement with capture records. Population expansion of Craseomys rufocanus during the LGC resulted in range extension and its current distribution, whereas the current range of Craseomys rex was derived from glacial refugia.
Morbidity and Mortality Risk Among People With Human Immunodeficiency Virus and Central or Visceral Adiposity: A Targeted Literature Review
Authors: Bjornson Alison M , Bedimo Roger J , Szabo Shelagh M , Rochon Hannah , Lee Daniel
Published: December 2024

Background

Given the known relationship between human immunodeficiency virus (HIV), antiretroviral therapies, and excess visceral adipose tissue (VAT), this review sought to characterize risk of negative health outcomes associated with excess VAT and increased waist circumference (WC) in people with HIV (PWH).

Methods

Comprehensive targeted literature searches were conducted in Medline/Embase (27 June 2022), identifying peer-reviewed articles and conference abstracts reporting on cohorts of PWH. Screening was guided by PECOS (Population, Exposure, Comparator, Outcomes, Study design) criteria. From the included studies, outcomes of interest including mortality and morbidity risk by VAT area and WC were extracted, overall, and by sex, race/ethnicity, and duration of HIV. Relationships between outcome and exposure variables were summarized.

Results

Thirty-five studies were included (sample size range: 31–1748 PWH). Twenty-five studies characterized the relationship between increased WC and negative health outcomes—cardiovascular disease (CVD), arteriosclerosis, hypertension, diabetes, hepatic fat and fibrosis, and cognitive impairment—among PWH. Fifteen studies reported on increased VAT and negative health outcomes: all-cause mortality, CVD, atherosclerosis, hepatic fat, and fibrosis. Importantly, there was a 2.1-times higher odds of 5-year all-cause mortality among PWH with the highest amount of VAT in the only study identified reporting on mortality. Among the studies characterizing the relationship between morbidity and VAT, for example, 1 found that, for each 10-cm2 increase in VAT, the risk of prevalent CVD increased by 1.05 (95% CI: 1.0–1.1) times.

Conclusions

WC may be a useful and cost-effective surrogate for visceral adiposity, which is an important marker of morbidity and mortality among PWH.
Admiring the Greeks with Roman eyes: F. A. Wolf, Quintilian, and the Latin roots of German philhellenism
Authors: Loporcaro Laura
Published: December 2024

This paper argues for the underlying importance of Latin learning in a key text of German philhellenism, Friedrich August Wolf’s ‘Darstellung der Alterthums-Wissenschaft’ (1807). It contends that Wolf supported his educational authority by modelling himself on the Roman rhetorical writer Quintilian, and that he drew on him to formulate the notion of a philological encyclopaedia. First, this paper uncovers how Wolf’s self-staging at the start of the ‘Darstellung’ channels Quintilian’s Institutio oratoria. Then, it shows that Wolf argued that Altertumswissenschaft was ‘scientific’ because it was ‘encyclopaedic’, and that he drew on Quintilian not necessarily to conceptualize, but to formulate, this conception. Uncovering the presence of Quintilian in Wolf’s ‘Darstellung’, an influential programmatic text that asserted the superiority of Greece over Rome, this paper argues for the persistence of Latin learning, just as it was dismissed, as a key irony underlying this foundational work of modern classical philology.
The Migrant Mother’s Silence in Her Mother Tongue as a Mothering Strategy
Authors: Kačkutė Eglė
Published: December 2024

Historically silenced, literary mothers’ voices are finally now being given their due, but it is noteworthy that migrant mothers’ literary voices are yet to be fully heard. This essay focuses on literary representations of migrant mothers who refuse to speak their own mother tongue to their children. It looks at two texts by women writers originating directly or indirectly from two post-Soviet Baltic states, Estonia and Lithuania. The texts in question are the novel Stalinin lehmät (Stalin’s Cows) (2003) by Sofi Oksanen and the essay “Motinų tylėjimas” (“The Silence of the Mothers”) (2004) by Dalia Staponkutė. Drawing on postcolonial theory, memory studies, and transnational feminist theory, I suggest that the migrant mother’s silence in her own mother tongue connotes several unarticulated realities: the trauma of colonization, the negotiation of post-Soviet migrant femininity, and patriarchal gender regimes. I argue that the migrant mothers represented in both texts withhold their mother tongue as a mothering strategy designed to socialize their children to successfully negotiate the transnational, multilingual spaces they will navigate as adults.
scEccDNAdb: an integrated single-cell eccDNA resource for human and mouse
Authors: Wang Wenqing , Zhao Xinyu , Ma Tianyu , Zhong Tengwei , Zheng Junnuo , Guo Zhiyun
Published: December 2024

Extrachromosomal circular DNA (eccDNA), an extrachromosomal circular structured DNA, is extensively found in eukaryotes. Investigating eccDNA at the single-cell level is crucial for understanding cellular heterogeneity, evolution, development, and specific cellular functions. However, high-throughput identification methods for single-cell eccDNA are complex, and the lack of mature, widely applicable technologies has resulted in limited resources. To address this gap, we built scEccDNAdb, a database based on single-cell whole-genome sequencing data. It contains 3 195 464 single-cell eccDNA entries from human and mouse samples, with annotations including oncogenes, typical enhancers, super-enhancers, CCCTC-binding factor-binding sites, single nucleotide polymorphisms, chromatin accessibility, expression quantitative trait loci, transcription factor binding sites, motifs, and structural variants. Additionally, it provides nine online analysis and visualization tools, which enable the creation of publication-quality figures through user-uploaded files. Overall, scEccDNAdb is a comprehensive database for analyzing single-cell eccDNA data across diverse cell types, tissues, and species.

Database URL: https://lcbb.swjtu.edu.cn/scEccDNAdb/
Near-complete telomere-to-telomere de novo genome assembly in Egyptian clover (Trifolium alexandrinum)
Authors: Sato Mitsuhiko P , Arafa Ramadan A , Rakha Mohamed T , Emeran Amero A , Isobe Sachiko , Shirasawa Kenta
Published: December 2024

Egyptian clover (Trifolium alexandrinum L.), also known as berseem clover, is an important forage crop to semi-arid conditions that was domesticated in ancient Egypt in 5,5000 BCE and introduced and well adapted to numerous countries including India, Pakistan, Turkey, and Mediterranean region. Despite its agricultural importance, genomic research on Egyptian clover has been limited to developing efficient modern breeding programs. In the present study, we constructed near-complete telomere-to-telomere-level genome assemblies for 2 Egyptian clover cultivars, Helaly and Fahl. Initial assemblies were established by using highly fidelity long-read technology. To extend sequence contiguity, we developed a gap-targeted sequencing (GAP-Seq) method, in which contig ends are targeted for sequencing to obtain long reads bridging 2 contigs. The total length of the resultant chromosome-level assemblies was 547.7 Mb for Helaly and 536.3 Mb for Fahl. These differences in sequence length can be attributed to the expansion of DNA transposons. Population genomic analysis using single-nucleotide polymorphisms revealed genomic regions highly differentiated between 2 cultivars and increased genetic uniformity within each cultivar. Gene ontologies associated with metabolic and biosynthetic processes and developmental processes were enriched in these genomic regions, indicating that these genes may determine the unique characteristics of each cultivar. Comprehensive genomic resources can provide valuable insights into genetic improvements in Egyptian clover and legume genomics.
The role of anthropogenic influences on a tropical lake ecosystem and its surrounding catchment: a case study of Lake Sentani
Authors: Nomosatryo Sulung , Lipus Daniel , Bartholomäus Alexander , Henny Cynthia , Ridwansyah Iwan , Sujarta Puguh , Yang Sizhong , Wagner Dirk , Kallmeyer Jens
Published: December 2024

Lake Sentani is a tropical lake in Indonesia, consisting of four interconnected sub-basins of different water depths. While previous work has highlighted the impact of catchment composition on biogeochemical processes in Lake Sentani, little is currently known about the microbiological characteristics across this unique ecosystem. With recent population growth in this historically rural area, the anthropogenic impact on Lake Sentani and hence its microbial life is also increasing. Therefore, we aimed to explore the influence of environmental and anthropogenic factors on the microbial diversity of Lake Sentani. Here, we present a detailed microbiological evaluation of Lake Sentani, analyzing 49 different sites across the lake, its tributary rivers and their river mouths to assess diversity and community structure using 16S rRNA gene sequencing. Our results reveal distinct communities in lake and river sediments, supporting the observed geochemical differences. Taxonomic assessment showed the potential impact of anthropogenic pressure along the northern, urbanized shore, as river and river mouth samples revealed high abundances of Bacteroidota, Firmicutes, and Cyanobacteria, which could be attributed to pollution and eutrophication. In contrast, lake sediment communities were dominated by Thermodesulfovibrionia, Methanomethylicia, Bathyarchaeia, and Thermoplasmata, suggesting sulfate reducing, thermophilic, acidophilic bacteria and methanogenic archaea to play an important role in tropical lake systems. This study provides novel insights into ecological functions of tropical lakes and contributes to the optimization of management strategies of Lake Sentani, ensuring its holistic preservation in the future.
Focusing on Caregiver Neglect: A Novel Strategy for Mistreatment of Older Adults Screening and Intervention
Authors: Rosen Tony , Shaw Amy , Elman Alyssa , Baek Daniel , Gottesman Elaine , Park Sophie , Costantini Helena , Cury Hincapie Mariana , Chang E-Shien , Hancock David , Jaret Adrienne D , Lees Haggerty Kristin , Burnes David , Lachs Mark S , Pillemer Karl , Czaja Sara J
Published: December 2024

Mistreatment of older adults is common and has serious health consequences but is underrecognized and underreported. Screening for mistreatment of older adults and initiation of intervention in primary care clinics may be helpful, but the value of existing tools is not supported by evidence. We argue that shifting the focus to individual subtypes of mistreatment of older adults can provide improved approaches to screening and ultimately to intervention. We focus on the example of caregiver neglect, the subtype associated with highest mortality. To develop caregiver neglect screening and intervention programs and to measure their effectiveness and impact, we assert that it is critical to: (1) define the phenomenon, (2) develop a conceptual model to explain why it occurs, (3) develop measurement strategies, and (4) systematically examine existing literature. We describe here the initial components of this development process.
Thou Shalt Not Conduct Research on Software? Text and Data Mining of Computer Programs in the Current EU Copyright Framework
Authors: Widła Bohdan
Published: December 2024

The proliferation of generative AI has steered the discussion about text and data mining (TDM) in copyright law towards the problem of generative models. However, generative AI is not the only case for TDM. Mining data from computer programs can improve defect detection, discover design patterns, facilitate maintenance, summarize code in natural language or identify security vulnerabilities. The potential of such research, and the risk of skewing its results due to inadequate data justifies a venture into the scope of permitted TDM activities in relation to software.

This article explores the intersection of TDM and the protection of computer programs in EU copyright law, focusing on the reproduction and alteration rights under the Software Directive. It argues that although among the new TDM exceptions and limitations in the Directive on Copyright in the Digital Single Market only the general one explicitly mentions computer programs, the research exception can also be applied if implemented carefully. This article also shows that computer programs can be reproduced in a way relevant to copyright law during TDM activities aimed at extracting data from traditional literary or artistic works. It offers an interpretation of Art. 5(1) of the Software Directive that prevents the misusing of copyright to thwart TDM in such scenarios. Finally, it analyses the diverging implementation strategies of TDM provisions adopted by EU Member States in the context of computer programs. By examining these issues, this article aims to clarify the scope of permissible TDM activities and advocate for policies that support research.
Integrated multi-omics analysis revealed the molecular networks and potential targets of cellular senescence in Alzheimer’s disease
Authors: Xu Yudi , Liu Shutong , Zhou Zhaokai , Qin Hongzhuo , Zhang Yuyuan , Zhang Ge , Ma Hongxuan , Han Xinwei , Liu Huimin , Liu Zaoqu
Published: December 2024

Cellular senescence (CS) is a hallmark of Alzheimer’s disease (AD). However, the mechanisms through which CS contributes to AD pathogenesis remain poorly understood. We found that CS level in AD was higher compared with the healthy control group. Transcriptome-based differential expression analysis identified 113 CS-related genes in blood and 410 in brain tissue as potential candidate genes involved in AD. To further explore the causal role of these genes, an integrative mendelian randomization analysis was conducted, combining AD genome-wide association study summary statistics with expression quantitative trait loci (eQTL) and DNA methylation quantitative trait loci (mQTL) data from blood samples, which identified five putative AD-causal genes (CENPW, EXOSC9, HSPB11, SLC44A2, and SLFN12) and 18 corresponding DNA methylation probes. Additionally, integrative analysis between eQTLs and mQTLs from blood uncovered two genes and 12 corresponding regulatory elements involved in AD. Furthermore, two genes (CDKN2B and ITGAV) were prioritized as putative causal genes in brain tissue and were validated through in vitro experiments. The multi-omics integration study revealed the potential role and underlying biological mechanisms of CS driven by genetic predisposition in AD. This study contributed to fundamental understanding of CS in AD pathogenesis and facilitated the identification of potential therapeutic targets for AD prevention and treatment.
Increased risk of subsequent antiphospholipid syndrome in patients with endometriosis
Authors: Chen Zhiyong , Cui Ran , Wang Shiow-Ing , Zhang Hua , Chen Miao , Wang Qian , Tong Qiang , Wei James Cheng-Chung , Dai Sheng-Ming
Published: December 2024

Background

Although autoimmune abnormalities are common in patients with endometriosis, it is unknown whether patients with endometriosis have a higher risk of developing antiphospholipid syndrome (APS).

Methods

We conducted a retrospective cohort study by using the multi-institutional research network TriNetX from 1 January 2012 to 31 December 2021. A total of 13 131 782 women aged 20–60 years from networks within the USA were included. The risks of APS were compared between an endometriosis cohort and a non-endometriosis cohort in subgroup analyses by age, obesity and systemic lupus erythematosus (SLE), and the sensitivity analysis was stratified by the presence or absence of a history of surgery of the uterus.

Results

After 1:1 propensity score matching, the endometriosis and non-endometriosis cohorts each included 50 078 participants. Compared to individuals without endometriosis, patients with endometriosis had a higher risk of incident APS (log-rank test, P < 0.001). The hazard ratios (HRs) ranged from 1.82 [APS within 30 days to 1 year after the index date, 95% confidence intervals (CIs) 1.40–2.53] to 2.44 (APS within 30 days to any time after the index date, 95% CI 1.65–3.61). In the subgroup analyses, an increased risk of APS was observed in all ages, White race, and subgroups without smoking, obesity, asthma, inflammatory bowel disease and SLE (HR range 1.85–2.84). Sensitivity analyses revealed that the risk of APS increased in patients without surgery history of the uterus.

Conclusions

Patients with endometriosis had a higher risk (2.84-fold) of developing APS. Future large-scale prospective studies are warranted to confirm our results.
Stability of Convex Spheres
Authors: Máximo Davi , Stufflebeam Hunter
Published: December 2024

We prove that strictly convex $2$-spheres, all of whose simple closed geodesics are close in length to $2\pi $, are $C^{0}$ Cheeger–Gromov close to the round sphere.
Modification of bone architecture following sleeve gastrectomy: a five-year follow-up
Authors: Maïmoun Laurent , Aouinti Safa , Puech Marion , Lefebvre Patrick , Humbert Ludovic , Deloze Mélanie , de Santa Barbara Pascal , Maïmoun-Nande Lisa , Boudousq Vincent , Cristol Jean-Paul , Renard Eric , Picot Marie-Christine , Mariano-Goulart Denis , Nocca David
Published: December 2024

Bariatric surgery induces a decrease in areal BMD (aBMD), but the long-term effect on trabecular and cortical volumetric BMD (vBMD) has not been well assessed. The main aim of this 5-yr longitudinal study was to investigate the changes following sleeve gastrectomy (SG) in aBMD, bone turnover markers, and trabecular and cortical vBMD. Forty-five patients with obesity were assessed before and 1, 2, and 5 yr after SG. Trabecular and cortical vBMD, cortical thickness, and structural parameters were assessed by 3D-Shaper software at the hip. Values of bone turnover markers peaked after 1 yr and decreased after 2 and 5 yr, but without returning to baseline values. aBMD decreased mostly at the femoral neck (−9.7%) and total hip (−10.7%) over the 5 yr, with the greatest loss occurring at 1 yr (−5.9% and −6.3%, respectively). A similar profile of decrease was observed for integral hip vBMD with significant decreases of 6.6%, 7.7%, and 10.7% after 1, 2, and 5 yr, mainly due to a reduction in the trabecular (10.5%, 12.0%, and 17.2%, respectively) rather than cortical (1.4%, 1.9%, and 2.9%, respectively) component. A modest decrease in mean cortical thickness (2.5%, 2.8%, and 3.9%, respectively) and an alteration in the structural parameters were concomitantly observed. Older age and greater body weight loss were the factors most associated with an increased loss of aBMD and vBMD. In conclusion, the study demonstrates that SG induces not only an alteration in bone turnover and aBMD, but also a reduction in vBMD at the hip, predominantly due to trabecular component deterioration as determined by 3D-Shaper software. The maintenance of bone deterioration for at least 5 yr—ie, after 4 yr of relative body weight stabilization or minimal weight regain—suggests the need for a therapeutic approach to preserve bone health in patients who undergo SG.