bluuebunny/crossref_metadata_2025_split huggingface dataset:
Techniques for investigating lncRNA transcript functions in neurodevelopment
Authors: Srinivas Tara , Siqueira Edilene , Guil Sonia 
Published: December 2023

AbstractLong noncoding RNAs (lncRNAs) are sequences of 200 nucleotides or more that are transcribed from a large portion of the mammalian genome. While hypothesized to have a variety of biological roles, many lncRNAs remain largely functionally uncharacterized due to unique challenges associated with their investigation. For example, some lncRNAs overlap with other genomic loci, are expressed in a cell-type-specific manner, and/or are differentially processed at the post-transcriptional level. The mammalian CNS contains a vast diversity of lncRNAs, and lncRNAs are highly abundant in the mammalian brain. However, interrogating lncRNA function in models of the CNS, particularly in vivo, can be complex and challenging. Here we review the breadth of methods used to investigate lncRNAs in the CNS, their merits, and the understanding they can provide with respect to neurodevelopment and pathophysiology. We discuss remaining challenges in the field and provide recommendations to assay lncRNAs based on current methods.
Research on oriented surface defect detection in the aircraft skin‐coating process based on an attention detector
Authors: Zhang Yongde , Wang Wei , Guo Zhonghua , Ji Yangchun 
Published: December 2023

AbstractAircraft coating process has been an important part in manufacturing process of modern aviation products. For coating defect detection, the manual observation with naked eyes is usually utilized, which leads to low production efficiency. In this paper, the authors propose the improved YOLOv5‐OBB with the channel‐spatial attention block (CSAB), feature pyramid non‐local module (FPNM) and structured sparsity slimming criterion (SSSC). The CSAB can pay more attention to effective channel information features from the channel dimension and the target information area from the spatial dimension. The effective non‐local module called FPNM is proposed to further improve the detection accuracy. The authors utilize the oriented bounding boxes (OBB) to reduce redundant background information for coating defect detection. In addition, the SSSC is proposed to achieve network slimming and trade‐off between the efficiency and accuracy. The experimental results on several datasets demonstrate the effectiveness of the authors’ scheme, which achieves superior performance.
3D non-LTE modeling of the stellar center-to-limb variation for transmission spectroscopy studies
Authors: Canocchi G. , Lind K. , Lagae C. , Pietrow A. G. M. , Amarsi A. M. , Kiselman D. , Andriienko O. , Hoeijmakers H. J. 
Published: December 2023

Context. Transmission spectroscopy is one of the most powerful techniques used to characterize transiting exoplanets, since it allows for the abundance of the atomic and molecular species in the planetary atmosphere to be measured. However, stellar lines may bias the determination of such abundances if their center-to-limb variations (CLVs) are not properly accounted for.
Aims. This paper aims to show that three-dimensional (3D) radiation hydrodynamic models and the assumption of non-local ther-modynamic equilibrium (non-LTE) line formation are required for an accurate modeling of the stellar CLV of the Na I D1 and K I resonance lines on transmission spectra.
Methods. We modeled the CLV of the Na I D1 and K I resonance lines in the Sun with 3D non-LTE radiative transfer. The synthetic spectra were compared to solar observations with high spatial and spectral resolution, including new data collected with the CRISP instrument at the Swedish 1-m Solar Telescope between µ = 0.1 and µ = 1.0.
Results. Our 3D non-LTE modeling of the Na I D1 resonance line at 5896 Å and the K I 7699 Å resonance line in the Sun is in good agreement with the observed CLV in the solar spectrum. Moreover, the simulated CLV curve for a Jupiter-Sun system inferred with a 3D non-LTE analysis shows significant differences from the one obtained from a 1D atmosphere. The latter does indeed tend to overestimate the amplitude of the transmission curve by a factor that is on the same order of magnitude as a planetary absorption depth (i.e., up to 0.2%).
Conclusions. This work highlights the fact that to correctly characterize exoplanetary atmospheres, 3D non-LTE synthetic spectra ought to be used to estimate the stellar CLV effect in transmission spectra of solar-like planet hosts. Moreover, since different spectral lines show different CLV curves for the same geometry of the planet-star system, it is fundamental to model the CLV individually for each line of interest. The work will be extended to other lines and FGK-type stars, allowing for synthetic high-resolution spectra to mitigate the stellar contamination of low-resolution planetary spectra, for example, those drawn from JWST.
Abundance of selected genes implicated in testicular functions in Camelus dromedarius with high and low epididymal semen quality
Authors: Rashad Dina E M , Ibrahim Sally , El-Sokary Mohamed M M , Mahmoud Karima Gh M , Abou El-Roos Mahmoud E A , Sosa Gamal A M , Kandiel Mohamed M M 
Published: December 2023

Abstract
Studying testicular genes’ expression may give key insights into precise regulation of its functions that influence epididymal sperm quality. The current study aimed to investigate the abundance of candidate genes involved in the regulation of testicular functions specially those regulate sperm function (PLA2G4D, SPP1, and CLUAP1), testicular steroidogenic function (ESR1 and AR), materials transport (AQP12B and LCN15), and defense mechanisms (DEFB110, GPX5, SOCS3, and IL6). Therefore, blood samples and testes with epididymis were collected from mature middle-aged (5–10 years) dromedary camels (n = 45) directly prior and after their slaughtering, respectively, during breeding season. Sera were evaluated for testosterone level and testicular biometry was measured with caliper. The epididymal tail semen was evaluated manually. Samples were distinguished based on testosterone level, testicular biometry, as well as epididymal semen features into high and low fertile groups. Total RNA was isolated from testicular tissues and gene expression was done using Quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR). Results revealed that testosterone levels were significantly (P &lt; 0.005) higher in camels with good semen quality than those of low quality. There was a significant (P &lt; 0.0001) increase in testicular weight, length, width, thickness, and volume in high fertile than low fertile camels. PLA2G4D, SPP1, CLUAP1, ESR1, AR, AQP12B, LCN15, DEFB110, GPX5, and SOCS3 genes were upregulated (P &lt; 0.001), and IL6 gene was downregulated (P &lt; 0.01) in the testes of high fertile camels compared to the low fertile one. Thus, it could be concluded that examined genes might be valuable monitors of testicular functional status and fertility in dromedary camels.
AKAP3-mediated type I PKA signaling is required for mouse sperm hyperactivation and fertility
Authors: Liang Zhongkun , Dai Chaowei , He Fenfen , Wang Yu , Huang Yihua , Li Heying , Wu Yongming , Hu Yafang , Xu Kaibiao 
Published: December 2023

AbstractThe protein kinase A (PKA) signaling pathway, which mediates protein phosphorylation, is important for sperm motility and male fertility. This process relies on A-kinase anchoring proteins that organize PKA and its signalosomes within specific subcellular compartments. Previously, it was found that the absence of A-kinase anchoring protein 3 (AKAP3) leads to multiple morphological abnormalities in mouse sperm. But how AKAP3 regulates sperm motility is yet to be elucidated. AKAP3 has two amphipathic domains, here named dual and RI, in its N-terminus. These domains are responsible for binding regulatory subunits I alpha (RIα) and II alpha (RIIα) of PKA and for RIα only, respectively. Here, we generated mutant mice lacking the dual and RI domains of AKAP3. It was found that the deletion of these domains caused male mouse infertile, accompanied by mild defects in the fibrous sheath of sperm tails. Additionally, the levels of serine/threonine phosphorylation of PKA substrates and tyrosine phosphorylation decreased in the mutant sperm, which exhibited a defect in hyperactivation under capacitation conditions. The protein levels of PKA subunits remained unchanged. But, interestingly, the regulatory subunit RIα was mis-localized from principal piece to midpiece of sperm tail, whereas this was not observed for RIIα. Further protein–protein interaction assays revealed a preference for AKAP3 to bind RIα over RIIα. Collectively, our findings suggest that AKAP3 is important for sperm hyperactivity by regulating type-I PKA signaling pathway mediated protein phosphorylation via its dual and RI domains.
To Whom Is the Institutional Chaplain Beholden? Reconciling the Christian Chaplain’s Tension of Identity With a Theology of Calling
Authors: Guthrie Michael 
Published: December 2023

Abstract
Professional chaplains have the unique opportunity to provide spiritual care within institutional settings where other types of pastoral care may not exist. Serving within these institutions presents special challenges, including tension between multiple identities and responsibilities. This tension can create conflict within the Christian chaplain, and confusion as to whom they are ultimately beholden. The first section of the article discusses what I see as the five identity-related tensions a professional chaplain may experience serving in an institution. The second section of the article outlines a Christian theology of calling built on the framework of Covenant Theology and God’s reconciling work of grace. This theology of calling orients the professional identity of the Christian chaplains, rooting them in a clear sense of their responsibilities within their institutional setting. Christian chaplains are beholden first to God and to the calling God places on their life. Proper orientation to that calling equips chaplains to reconcile any cognitive dissonance caused by identity-related tensions, thus opening up a richer spiritual dialogue with God as they live out their kingdom-advancing mission.
Gallic acid triphenylphosphonium derivatives TPP+-C10 and TPP+-C12 inhibit mitochondrial function in Candida albicans exerting antifungal and antibiofilm effects
Authors: Valderrama Victoria , Sánchez Paula , Delso Macarena , Díaz-Dosque Mario , Escobar Alejandro , Budini Mauricio , Catalán Mabel , Vivar Raúl , López-Muñoz Rodrigo , Jara José A , Molina-Berríos Alfredo 
Published: December 2023

Abstract

Aims
To evaluate the antifungal and antibiofilm activity of gallic acid derivatives TPP+-C10 and TPP+-C12 and their effects on mitochondrial function on two Candida albicans reference strains (ATCC 90029 and ATCC 10231).

Methods and results
First, we determined minimal inhibitory concentration (MIC) using a microdilution assay. Both compounds exerted antifungal effects, and their MICs ranged from 3.9 to 13 µM, with no statistically significant differences between them (P &gt; 0.05, t-test). These concentrations served as references for following assays. Subsequently, we measured oxygen consumption with a Clark electrode. Our observations revealed that both drugs inhibited oxygen consumption in both strains with TPP+-C12 exerting a more pronounced inhibitory effect. We then employed flow cytometry with TMRE as a probe to assess mitochondrial membrane potential. For each strain assayed, the compounds induced a decay in transmembrane potential by 75%–90% compared to the control condition (P &lt; 0.05, ANOVA). Then, we measured ATP levels using a commercial kit. TPP+-C12 showed a 50% decrease of ATP content (P &lt; 0.05 ANOVA), while TPP+-C10 exhibited a less pronounced effect. Finally, we assessed the antibiofilm effect using the MTT reduction assay. Both compounds were effective, but TPP+-C12 displayed a greater potency, requiring a lower concentration to inhibit 50% of biofilms viability (P &lt; 0.05, t-test).

Conclusions
Derivatives of gallic acid linked to a TPP+ group exert antifungal and antibiofilm activity through impairment of mitochondrial function in C. albicans.
Orally administered Streptococcus thermophilus YIT 2001 is a vehicle for the delivery of glutathione, a reactive reduced thiol, to the intestine
Authors: Yamamoto Yu , Maki Koh , Kusuhara Shiro , Yokoi Wakae , Tochiya Kaoru , Okumura Takekazu , Ito Masahiko , Miyazaki Kouji , Harada Katsuhisa , Takagi Akimitsu 
Published: December 2023

Abstract

Aims
We aimed to analyze the behavior of cellular glutathione of Streptococcus thermophilus strain YIT 2001 (ST-1) in the gastrointestinal environment to understand how orally administered glutathione in ST-1 cells is delivered stably to the intestine in a reactive form, which is essential for its systemic bioavailability against lipid peroxidation.

Methods and results
Intracellular glutathione was labeled with L-cysteine-containing stable isotopes. ST-1 cells from fresh culture or lyophilized powder were treated with simulated gastric and intestinal juices for 60 min each. The release of intracellular glutathione in digestive juices was quantified via LC–MS/MS. Most of the cellular glutathione was retained in the gastric environment and released in response to exposure to the gastrointestinal environment. During digestion, the membrane permeability of propidium iodide increased significantly, especially when cells were exposed to cholate, without change in the cell wall state.

Conclusions
ST-1 cells act as vehicles to protect intracellular reactive components, such as glutathione, from digestive stress, and release them in the upper intestine owing to the disruption of membrane integrity induced by bile acid.
Leveraging the digital layer: the strength of weak and strong ties in bridging geographic and cognitive distances
Authors: Abbasiharofteh Milad , Kinne Jan , Krüger Miriam 
Published: December 2023

Abstract
Firms may seek non-redundant information through inter-firm relations beyond their geographic and cognitive boundaries (i.e., relations with firms in other regions and active in different fields). Little is known about the conditions under which firms benefit from this high-risk/high-gain strategy. We created a digital layer of 600,000 German firms by using their websites’ textual and relational content. Our results suggest that strong relations (relations with common third partners) between firms from different fields and inter-regional relations are positively associated with a firm’s innovation level. We also found that a specific combination of weak and strong relations confers greater innovation benefits.
Viscoacoustic least-squares reverse-time migration using the L1-2 norm sparsity constraint
Authors: Zhang Mingkun , Wang Lingqian , Chen Hanming , Zhou Hui , Liu Peng 
Published: December 2023

Abstract
Least-squares reverse-time migration (LSRTM) has become an advanced technique for complex structures imaging of the subsurface, as it can provide a higher resolution and more balanced amplitude migrated image than conventional reverse-time migration (RTM). However, the intrinsic attenuation of the subsurface introduces amplitude attenuation and phase dispersion of the seismic wavefield, which leads to an inexact inverted image kinematically and dynamically. Moreover, the imperfect geometry, limited bandwidth of seismic data, and inappropriate modeling kernel etc., would inevitably introduce two side-effects in the migrated image, resulting in degradation of LSRTM imaging potential. To alleviate these issues, we present a data-domain sparsity constraint viscoacoustic LSRTM algorithm in this paper. In particular, we use the decoupled constant Q fractional Laplacian viscoacoustic wave equation as the modeling kernel to describe the attenuation effects of the subsurface, while a model constraint constructed in the misfit function via the L1-2 norm is carried out to clear the migrated artifacts and boost the imaging resolution. Thanks to the excellent performance in sparsity, the drawbacks of unconstrained LSRTM can be effectively mitigated by the L1-2 norm-based regularization. In this paper, we adopt the alternating direction of multipliers method to iteratively address the constrained L1-2 minimization problem by implementing a proximal operator, and three synthetic examples are used to evaluate the effectiveness and practicability of the proposed strategy. Migration results prove that the proposed scheme can effectively compensate for the attenuation effects, improve the resolution, and suppress the migration artifacts of inverted images even in the complex imaging situations.
Love and Horror: ‘Ircastrensis’ Unmasked
Authors: Freeman Janet Ing 
Published: December 2023

Abstract
This note identifies, for the first time, the author of Love and Horror, a mock-heroic parody of the gothic novel published under the pseudonym ‘Ircastrensis’ in 1812. The Revd Henry Barry (1781-1850) wrote at least one other novel before settling into a comfortable life as a Wiltshire rector and unsuccessful dabbler in British history and Shakespearean emendation; among his several children was the much better known Victorian novelist Emma Newby (1826-1899), who in 1862 edited her father’s final book, a ‘manual of happiness’.
Fe ii fluorescence in main-sequence K-dwarfs
Authors: Eriksson M 
Published: December 2023

ABSTRACT
Main-sequence K-dwarfs possess strong emission in the form of the H i Ly α line. There is a close coincidence between the energy corresponding to the transitions H i 1s-2p and Fe ii (5D)5s 4D5/2–(5D)5p 4D5/2. Singly ionized iron has been confirmed being pumped by photo-excitation by accidental resonance (PAR) in planetary nebulae, symbiotic stars, K-giants, and active galactic nebulae. I investigate in this work whether PAR can occur in the atmospheres of main-sequence K-dwarfs, which do not possess the large extended atmospheres of the late-type K-giants. Specifically a search for possible Fe ii fluorescence lines is conducted. For the case when I can confirm PAR, I estimate the total flux leaving the stars in the form of Fe ii fluorescence. I search for emission lines from the Fe ii (5D)5p 4D5/2 level. Since those of these lines with the largest branching fractions correspond to lines at wavelengths covered by the Far Ultraviolet Spectroscopic Explorer (FUSE) satellite, a search for archival FUSE spectra from K-dwarfs within 20 ly from the sun is conducted. I retrieve and analyse FUSE spectra for four of these K-dwarfs. In each case I can confirm PAR, I fit the H i Ly α line in Hubble Space Telescope spectra recorded with the Space Telescope Imaging Spectrograph, in order to estimate the efficiency of the PAR mechanism. I can now confirm Fe ii fluorescence in the two closest K-dwarfs, Alpha Centauri B, and Epsilon Eridani. The total power leaving as Fe ii fluorescence are 4.9 × 1017 and 1.30 × 1018 W respectively.
The efficacy of rituximab plus belimumab or telitacicept in refractory lupus nephritis
Authors: Chen Yiting , Shi Nan , Lei Xin , Ren Pingping , Lan Lan , Chen Liangliang , Wang Yaomin , Xu Ying , Lin Yuxin , Chen Jianghua , Han Fei 
Published: December 2023

Abstract

Objective
Lupus nephritis is a severe and common complication of systemic lupus erythematosus (SLE). The pathogenesis of lupus nephritis is characterized by B-cell activation and autoantibody formation. Rituximab and belimumab, as well as telitacicept, target B cells through different mechanisms, potentially exerting a synergistic effect in the treatment of lupus nephritis. This study aims to investigate the efficacy and safety of treatment with rituximab followed by belimumab or telitacicept in the management of refractory lupus nephritis.

Methods
We conducted a single-center, open-label, retrospective study, including 25 patients with refractory lupus nephritis. All patients received combination therapy with rituximab in individualized dosages to achieve peripheral B-cell depletion, and then followed by belimumab or telitacicept. The follow-up period was at least 12 months, and the primary end point was renal remission rate at the last follow-up.

Results
During a median follow-up of 19 (13, 29) months, 20 of 25 (80%) patients achieved objective remission (OR), including 19 (76%) patients achieved complete renal response (CRR). After rituximab (712 ± 416mg in average), 18 patients received belimumab and seven patients received telitacicept. In the rituximab plus telitacicept group, all patients achieved CRR; while in the rituximab plus belimumab group, 12 (66.7%) patients achieved CRR and 13 (72.2%) patients achieved OR. The mean SLEDAI-2K score decreased from 15 ± 6 to 6 ± 6, representing an average reduction of 60%. At the last follow-up, 18/25 (72%) had prednisone ≤ 5 mg/d or even discontinued prednisone use. Adverse effects were mainly immunoglobulin deficiency, respiratory tract infection, urinary tract infections, and rash. No death occurred.

Conclusions
Rituximab followed by belimumab or telitacicept may be effective in inducing remission in refractory lupus nephritis, with tolerable adverse effects.
Shelterin dysfunction promotes CD4+ T cell senescence in Behçet’s disease
Authors: Shi Jing , Zhang Menghao , Zhang Lili , Yu Xin , Sun Luxi , Liu Jinjing , Zhao Yan , Zheng Wenjie 
Published: December 2023

Abstract

Objectives
To investigate the potential role of shelterin dysfunction in naïve CD4+ T cells in the pathogenesis of Behçet’s disease (BD).

Methods
Naïve CD4+ T cells were isolated from 40 BD patients and 40 sex- and age-matched healthy controls (HC). Senescent profiles, shelterin subunits expression, telomere length, telomerase activity and critical DNA damage response (DDR) were evaluated. Telomere repeat factor-2 (TRF2) silencing was conducted for further validation.

Results
Compared with HC, BD patients had significantly decreased naïve CD4+ T cells, increased cell apoptosis, senescence, and productions of TNF-α and IFN-γ upon activation. Notably, BD naïve CD4+ T cells had shortened telomere, impaired telomerase activity, and expressed lower levels of shelterin subunits TRF2, TRF1- and TRF2-Interacting Nuclear Protein 2 (TIN2) and Repressor/Activator Protein 1 (RAP1). Furthermore, BD naïve CD4+ T cells exhibited significantly increased DDR, evidenced by elevated phosphorylated ataxia telangiectasia (AT) mutated (pATM), phosphorylated p53 (pp53) and p21. Finally, TRF2 silencing markedly upregulated DDR, apoptosis and proinflammatory cytokines production in HC naïve CD4+ T cells.

Conclusion
Our study demonstrated that TRF2 deficiency in BD naïve CD4+ T cells promoted cell apoptosis and senescence, leading to proinflammatory cytokines overproduction. Therefore, restoring TRF2 might be a promising therapeutic strategy for BD.