bluuebunny/crossref_metadata_2025_split huggingface dataset:
Schur line defect correlators and giant graviton expansion
Authors: Beccaria M. 
Published: June 2024

Abstract
We consider Schur line defect correlators in four dimensional $$ \mathcal{N} $$
N
= 4 U(N) SYM and their giant graviton expansion encoding finite N corrections to the large N limit. We compute in closed form the single giant graviton contribution to correlators with general insertions of $$ \frac{1}{2} $$

1
2

-BPS charged Wilson lines. For the 2-point function with fundamental and anti-fundamental Wilson lines, we match the result from fluctuations of two half-infinite strings ending on the giant graviton, recently proposed in arXiv:2403.11543. In particular, we prove exact factorization of the defect contribution with respect to wrapped D3 brane fluctuations representing the single giant graviton correction to the undecorated Schur index. This follows from a finite-difference representation of the Schur line defect index in terms of the index without defects, and similar factorization holds quite generally for more complicated defect configurations. In particular, the single giant graviton contribution to the 4-point function with two fundamental and two anti-fundamental lines is computed and discussed in this perspective.
Prostaglandin I2 signaling prevents angiotensin II-induced atrial remodeling and vulnerability to atrial fibrillation in mice
Authors: Zhang Yue , Yuan Meng , Cai Wenbin , Sun Weiyan , Shi Xuelian , Liu Daiqi , Song Wenhua , Yan Yingqun , Chen Tienan , Bao Qiankun , Zhang Bangying , Liu Tong , Zhu Yi , Zhang Xu , Li Guangping 
Published: June 2024

AbstractAtrial fibrillation (AF) is the most common arrhythmia, and atrial fibrosis is a pathological hallmark of structural remodeling in AF. Prostaglandin I2 (PGI2) can prevent the process of fibrosis in various tissues via cell surface Prostaglandin I2 receptor (IP). However, the role of PGI2 in AF and atrial fibrosis remains unclear. The present study aimed to clarify the role of PGI2 in angiotensin II (Ang II)-induced AF and the underlying molecular mechanism. PGI2 content was decreased in both plasma and atrial tissue from patients with AF and mice treated with Ang II. Treatment with the PGI2 analog, iloprost, reduced Ang II-induced AF and atrial fibrosis. Iloprost prevented Ang II-induced atrial fibroblast collagen synthesis and differentiation. RNA-sequencing analysis revealed that iloprost significantly attenuated transcriptome changes in Ang II-treated atrial fibroblasts, especially mitogen-activated protein kinase (MAPK)-regulated genes. We demonstrated that iloprost elevated cAMP levels and then activated protein kinase A, resulting in a suppression of extracellular signal-regulated kinase1/2 and P38 activation, and ultimately inhibiting MAPK-dependent interleukin-6 transcription. In contrast, cardiac fibroblast-specific IP-knockdown mice had increased Ang II-induced AF inducibility and aggravated atrial fibrosis. Together, our study suggests that PGI2/IP system protects against atrial fibrosis and that PGI2 is a therapeutic target for treating AF.The prospectively registered trial was approved by the Chinese Clinical Trial Registry. The trial registration number is ChiCTR2200056733. Data of registration was 2022/02/12.
Structure, regulation, and mechanisms of nonmuscle myosin-2
Authors: Chinthalapudi Krishna , Heissler Sarah M. 
Published: June 2024

AbstractMembers of the myosin superfamily of molecular motors are large mechanochemical ATPases that are implicated in an ever-expanding array of cellular functions. This review focuses on mammalian nonmuscle myosin-2 (NM2) paralogs, ubiquitous members of the myosin-2 family of filament-forming motors. Through the conversion of chemical energy into mechanical work, NM2 paralogs remodel and shape cells and tissues. This process is tightly controlled in time and space by numerous synergetic regulation mechanisms to meet cellular demands. We review how recent advances in structural biology together with elegant biophysical and cell biological approaches have contributed to our understanding of the shared and unique mechanisms of NM2 paralogs as they relate to their kinetics, regulation, assembly, and cellular function.
Phospholipid scramblase 1: an essential component of the nephrocyte slit diaphragm
Authors: Castillo-Mancho Vicente , Atienza-Manuel Alexandra , Sarmiento-Jiménez Jorge , Ruiz-Gómez Mar , Culi Joaquim 
Published: June 2024

AbstractBlood ultrafiltration in nephrons critically depends on specialized intercellular junctions between podocytes, named slit diaphragms (SDs). Here, by studying a homologous structure found in Drosophila nephrocytes, we identify the phospholipid scramblase Scramb1 as an essential component of the SD, uncovering a novel link between membrane dynamics and SD formation. In scramb1 mutants, SDs fail to form. Instead, the SD components Sticks and stones/nephrin, Polychaetoid/ZO-1, and the Src-kinase Src64B/Fyn associate in cortical foci lacking the key SD protein Dumbfounded/NEPH1. Scramb1 interaction with Polychaetoid/ZO-1 and Flotillin2, the presence of essential putative palmitoylation sites and its capacity to oligomerize, suggest a function in promoting SD assembly within lipid raft microdomains. Furthermore, Scramb1 interactors as well as its functional sensitivity to temperature, suggest an active involvement in membrane remodeling processes during SD assembly. Remarkably, putative Ca2+-binding sites in Scramb1 are essential for its activity raising the possibility that Ca2+ signaling may control the assembly of SDs by impacting on Scramb1 activity.
Disrupting Smad3 potentiates immunostimulatory function of NK cells against lung carcinoma by promoting GM-CSF production
Authors: Lian Guang-Yu , Wang Qing-Ming , Mak Thomas Shiu-Kwong , Huang Xiao-Ru , Yu Xue-Qing , Lan Hui-Yao 
Published: June 2024

AbstractThrough Smad3-dependent signalings, transforming growth factor-β (TGF-β) suppresses the development, maturation, cytokine productions and cytolytic functions of NK cells in cancer. Silencing Smad3 remarkably restores the cytotoxicity of NK-92 against cancer in TGF-β-rich microenvironment, but its effects on the immunoregulatory functions of NK cells remain obscure. In this study, we identified Smad3 functioned as a transcriptional repressor for CSF2 (GM-CSF) in NK cells. Therefore, disrupting Smad3 largely mitigated TGF-β-mediated suppression on GM-CSF production by NK cells. Furthermore, silencing GM-CSF in Smad3 knockout NK cells substantially impaired their anti-lung carcinoma effects. In-depth study demonstrated that NK-derived GM-CSF strengthened T cell immune responses by stimulating dendritic cell differentiation and M1 macrophage polarization. Meanwhile, NK-derived GM-CSF promoted the survival of neutrophils, which in turn facilitated the terminal maturation of NK cells, and subsequently boosted NK-cell mediated cytotoxicity against lung carcinoma. Thus, Smad3-silenced NK-92 (NK-92-S3KD) may serve as a promising immunoadjuvant therapy with clinical translational value given its robust cytotoxicity against malignant cells and immunostimulatory functions to reinforce the therapeutic effects of other immunotherapies.
Optimization of an architected composite with tailored graded properties
Authors: Casalotti Arnaldo , D’Annibale Francesco , Rosi Giuseppe 
Published: June 2024

AbstractThe aim of the present study is to design a solid material with specific and tailored mechanical properties through a suitably defined design framework and to evaluate the effectiveness of different microstructure geometries in an engineering perspective. To these ends, topology optimization algorithms are applied on a 2D homogenized equivalent model of a periodic structure. The design framework, developed in a previous work for 2D lattices made of regular hexagons, is here expanded and validated also in the cases of circular and square unit cells. The proposed approach involves optimizing porosity distribution of a homogenized equivalent solid, obtained through a Bloch–Floquet-based analysis, within a 2D lattice of regular unit cells forming the core element of a sandwich panel. Finite-element analyses on homogenized and fine structural models are carried out in order to validate the procedure, beyond the particular choice of the unit cell geometry and to detect its effectiveness and limits.
Application of a robust MALDI mass spectrometry approach for bee pollen investigation
Authors: Braglia Chiara , Alberoni Daniele , Di Gioia Diana , Giacomelli Alessandra , Bocquet Michel , Bulet Philippe 
Published: June 2024

AbstractPollen collected by pollinators can be used as a marker of the foraging behavior as well as indicate the botanical species present in each environment. Pollen intake is essential for pollinators’ health and survival. During the foraging activity, some pollinators, such as honeybees, manipulate the collected pollen mixing it with salivary secretions and nectar (corbicular pollen) changing the pollen chemical profile. Different tools have been developed for the identification of the botanical origin of pollen, based on microscopy, spectrometry, or molecular markers. However, up to date, corbicular pollen has never been investigated. In our work, corbicular pollen from 5 regions with different climate conditions was collected during spring. Pollens were identified with microscopy-based techniques, and then analyzed in MALDI-MS. Four different chemical extraction solutions and two physical disruption methods were tested to achieve a MALDI-MS effective protocol. The best performance was obtained using a sonication disruption method after extraction with acetic acid or trifluoroacetic acid. Therefore, we propose a new rapid and reliable methodology for the identification of the botanical origin of the corbicular pollens using MALDI-MS. This new approach opens to a wide range of environmental studies spanning from plant biodiversity to ecosystem trophic interactions.
Graphical Abstract
Quantitative proteome-wide O-glycoproteomics analysis with FragPipe
Authors: Polasky Daniel A. , Lu Lei , Yu Fengchao , Li Kai , Shortreed Michael R. , Smith Lloyd M. , Nesvizhskii Alexey I. 
Published: June 2024

Abstract
Identification of O-glycopeptides from tandem mass spectrometry data is complicated by the near complete dissociation of O-glycans from the peptide during collisional activation and by the combinatorial explosion of possible glycoforms when glycans are retained intact in electron-based activation. The recent O-Pair search method provides an elegant solution to these problems, using a collisional activation scan to identify the peptide sequence and total glycan mass, and a follow-up electron-based activation scan to localize the glycosite(s) using a graph-based algorithm in a reduced search space. Our previous O-glycoproteomics methods with MSFragger-Glyco allowed for extremely fast and sensitive identification of O-glycopeptides from collisional activation data but had limited support for site localization of glycans and quantification of glycopeptides. Here, we report an improved pipeline for O-glycoproteomics analysis that provides proteome-wide, site-specific, quantitative results by incorporating the O-Pair method as a module within FragPipe. In addition to improved search speed and sensitivity, we add flexible options for oxonium ion-based filtering of glycans and support for a variety of MS acquisition methods and provide a comparison between all software tools currently capable of O-glycosite localization in proteome-wide searches.

Graphical Abstract
Root stacks and periodic decompositions
Authors: Bodzenta A. , Donovan W. 
Published: June 2024

AbstractFor an effective Cartier divisor D on a scheme X we may form an $${n}^{\text {th}}$$

n

th

root stack. Its derived category is known to have a semiorthogonal decomposition with components given by D and X. We show that this decomposition is $$2n$$

2
n

-periodic. For $$n=2$$

n
=
2

this gives a purely triangulated proof of the existence of a known spherical functor, namely the pushforward along the embedding of D. For $$n > 2$$

n
>
2

we find a higher spherical functor in the sense of recent work of Dyckerhoff et al. (N-spherical functors and categorification of Euler’s continuants. arXiv:2306.13350, 2023). We use a realization of the root stack construction as a variation of GIT, which may be of independent interest.
Two protocols for the detection of oleaginous bacteria using Oil Red O
Authors: Silva Roxana A. , Hernández Martín A. , Kalscheuer Rainer , Steinbüchel Alexander , Alvarez Héctor M. 
Published: June 2024

Abstract
The selection of oleaginous bacteria, potentially applicable to biotechnological approaches, is usually carried out by different expensive and time-consuming techniques. In this study, we used Oil Red O (ORO) as an useful dye for staining of neutral lipids (triacylglycerols and wax esters) on thin-layer chromatography plates. ORO could detect minimal quantities of both compounds (detection limit, 0.0025 mg of tripalmitin or 0.005 mg of cetylpalmitate). In addition, we developed a specific, rapid, and inexpensive screening methodology to detect triacylglycerol-accumulating microorganisms grown on the agar plate. This staining methodology detected 9/13 strains with a triacylglycerol content higher than 20% by cellular dry weight. ORO did not stain polyhydroxyalkanoates-producing bacteria. The four oleaginous strains not detected by this screening methodology exhibited a mucoid morphology of their colonies. Apparently, an extracellular polymeric substance produced by these strains hampered the entry of the lipophilic dye into cells. The utilization of the developed screening methodology would allow selecting of oleaginous bacteria in a simpler and faster way than techniques usually used nowadays, based on unspecific staining protocols and spectrophotometric or chromatographic methods. Furthermore, the use of ORO as a staining reagent would easily characterize the neutral lipids accumulated by microorganisms as reserve compounds.

Key points
• Oil Red O staining is specific for triacylglycerols
• Oil Red O staining is useful to detect oleaginous bacteria
• Fast and inexpensive staining to isolate oleaginous bacteria from the environment
Effects of the pleiotropic regulator DasR on lincomycin production in Streptomyces lincolnensis
Authors: Pai Huihui , Liu Yiying , Zhang Chuanbo , Su Jianyu , Lu Wenyu 
Published: June 2024

Abstract
The lincoamide antibiotic lincomycin, derived from Streptomyces lincolnensis, is widely used for the treatment of infections caused by gram-positive bacteria. As a common global regulatory factor of GntR family, DasR usually exists as a regulatory factor that negatively regulates antibiotic synthesis in Streptomyces. However, the regulatory effect of DasR on lincomycin biosynthesis in S. lincolnensis has not been thoroughly investigated. The present study demonstrates that DasR functions as a positive regulator of lincomycin biosynthesis in S. lincolnensis, and its overexpression strain OdasR exhibits a remarkable 7.97-fold increase in lincomycin production compared to the wild-type strain. The effects of DasR overexpression could be attenuated by the addition of GlcNAc in the medium in S. lincolnensis. Combined with transcriptome sequencing and RT-qPCR results, it was found that most structural genes in GlcNAc metabolism and central carbon metabolism were up-regulated, but the lincomycin biosynthetic gene cluster (lmb) were down-regulated after dasR knock-out. However, DasR binding were detected with the DasR responsive elements (dre) of genes involved in GlcNAc metabolism pathway through electrophoretic mobility shift assay, while they were not observed in the lmb. These findings will provide novel insights for the genetic manipulation of S. lincolnensis to enhance lincomycin production.

Key points
• DasR is a positive regulator that promotes lincomycin synthesis and does not affect spore production
• DasR promotes lincomycin production through indirect regulation
• DasR correlates with nutrient perception in S. lincolnensis
Enhanced bioenergetic cellular activity with metabolic switch to aerobic glycolysis in Keloid and Folliculitis Keloidalis Nuchae
Authors: Chalwa Temwani , Lebeko Maribanyana , Matobole Relebohile , P Khumalo Nonhlanhla , Bayat Ardeshir 
Published: June 2024

AbstractKeloid scars and folliculitis keloidalis nuchae (FKN) are benign fibroproliferative dermal lesions of unknown aetiology and ill-defined treatment, which typically present in genetically susceptible individuals. Their pathognomonic hallmarks include local aggressive invasive behaviour plus high recurrence post-therapy. In view of this, we investigated proliferative and key parameters of bioenergetic cellular characteristics of site-specific keloid-derived fibroblasts (intra(centre)- and peri(margin)-lesional) and FKN compared to normal skin and normal flat non-hypertrophic scar fibroblasts as negative controls.The results showed statistically significant (P < 0.01) and variable growth dynamics with increased proliferation and migration in keloid fibroblasts, while FKN fibroblasts showed a significant (P < 0.001) increase in proliferation but similar migration profile to controls. A statistically significant metabolic switch towards aerobic glycolysis in the fibroblasts from the disease conditions was noted. Furthermore, an increase in basal glycolysis with a concomitant increase in the cellular maximum glycolytic capacity was also demonstrated in perilesional keloid and FKN fibroblasts (P < 0.05). Mitochondrial function parameters showed increased oxidative phosphorylation in the disease conditions (P < 0.05) indicating functional mitochondria. These findings further suggest that Keloids and FKN demonstrate a switch to a metabolic phenotype of aerobic glycolysis. Increased glycolytic flux inhibition is a potential mechanistic basis for future therapy.
Outcome measurements in epidermal necrolysis: a systematic review
Authors: Libson Karissa , Mehta Nina , Kirven Rachel , Korman Abraham M. , Kaffenberger Benjamin H. 
Published: June 2024

AbstractSteven Johnson Syndrome (SJS) and Toxic Epidermal Necrolysis (TEN), grouped together under the terminology of epidermal necrolysis (EN), are a spectrum of life-threatening dermatologic conditions. A lack of standardization and validation for existing endpoints has been identified as a key barrier to the comparison of these therapies and development of evidenced-based treatment. Following PRISMA guidelines, we conducted a systematic review of prospective studies involving systemic or topical treatments for EN, including dressing and ocular treatments. Outcomes were separated into mortality assessment, cutaneous outcomes, non-cutaneous clinical outcomes, and mucosal outcomes. The COSMIN Risk of Bias tool was used to assess the quality of studies on reliability and measurement error of outcome measurement instruments. Outcomes across studies assessing treatment in the acute phase of EN were varied. Most data came from prospective case reports and cohort studies representing the lack of available randomized clinical trial data available in EN. Our search did not reveal any EN-specific validated measures or scoring tools used to assess disease progression and outcomes. Less than half of included studies were considered “adequate” for COSMIN risk of bias in reliability and measurement error of outcome measurement instruments. With little consensus about management and treatment of EN, consistency and validation of measured outcomes is of the upmost importance for future studies to compare outcomes across treatments and identify the most effective means of combating the disease with the highest mortality managed by dermatologists.
Lifestyle and medical conditions in relation to ALS risk and progression—an introduction to the Swedish ALSrisc Study
Authors: Chourpiliadis Charilaos , Seitz Christina , Lovik Anikó , Joyce Emily E. , Pan Lu , Hu Yihan , Kläppe Ulf , Samuelsson Kristin , Press Rayomand , Ingre Caroline , Fang Fang 
Published: June 2024

Abstract
Background
This study was an introduction to the Swedish ALSrisc Study and explored the association of lifestyle and medical conditions, with risk and progression of amyotrophic lateral sclerosis (ALS).

Methods
We included 265 newly diagnosed ALS patients during 2016–2022 in Stockholm and 207 ALS-free siblings and partners of the patients as controls. Information on body mass index (BMI), smoking, and history of head injuries, diabetes mellitus, hypercholesterolemia, and hypertension was obtained through the Euro-MOTOR questionnaire at recruitment. Patients were followed from diagnosis until death, invasive ventilation, or November 30, 2022.

Results
Higher BMI at recruitment was associated with lower risk for ALS (OR 0.89, 95%CI 0.83–0.95), especially among those diagnosed after 65 years. One unit increase in the average BMI during the 3 decades before diagnosis was associated with a lower risk for ALS (OR 0.94, 95%CI 0.89–0.99). Diabetes was associated with lower risk of ALS (OR 0.38, 95%CI 0.16–0.90), while hypercholesterolemia was associated with higher risk of ALS (OR 2.10, 95%CI 1.13–3.90). Higher BMI at diagnosis was associated with lower risk of death (HR 0.91, 95%CI 0.84–0.98), while the highest level of smoking exposure (in pack-years) (HR 1.90, 95%CI 1.20–3.00), hypercholesterolemia (HR 1.84, 95%CI 1.06–3.19), and hypertension (HR 1.76, 95%CI 1.03–3.01) were associated with higher risk of death, following ALS diagnosis.

Conclusions
Higher BMI and diabetes were associated with lower risk of ALS. Higher BMI was associated with lower risk of death, whereas smoking (especially in high pack-years), hypercholesterolemia, and hypertension were associated with higher risk of death after ALS diagnosis.
Variability of flow-mediated dilation across lower and upper limb conduit arteries
Authors: Daniele Alessio , Lucas Samuel J. E. , Rendeiro Catarina 
Published: June 2024

AbstractEndothelial dysfunction is an early predictor of atherosclerosis and cardiovascular disease. Flow-mediated dilation (FMD) is the gold standard to assess endothelial function in humans. FMD reproducibility has been mainly assessed in the brachial artery (BA) with limited research in lower limb arteries. The purpose of this study was to compare FMD reproducibility in the upper limb BA and lower limb superficial femoral artery (SFA) in young healthy adults.Fifteen young healthy adults (nine males; six females) underwent FMD, resting diameter, velocity, and shear rate measurements on three occasions to determine intra-and inter-day reproducibility in both BA and SFA, assessed by coefficient of variation (CV), intraclass correlation coefficient (ICC), and Bland–Altman plots.BA FMD CVs (intra-day: 4.2%; inter-day: 8.7%) and ICCs (intra-day: 0.967; inter-day: 0.903) indicated excellent reproducibility and reliability, while for SFA FMD, both CVs (intra-day: 11.6%; inter-day: 26.7%) and ICCs (intra-day: 0.898; inter-day: 0.651) showed good/moderate reproducibility and reliability. BA FMD was significantly more reproducible than SFA FMD (p < 0.05). Diameter reproducibility was excellent and similar between arteries, while resting velocity and shear rate have lower reproducibility in the BA compared to SFA. Bland–Altman plots displayed no proportional and fixed bias between measurements.In summary, SFA FMD is less reproducible than BA FMD, with identical volume of ultrasound training. Given the increasing interest in using SFA FMD to test the efficacy of interventions targeting lower limb’s vascular health and as a potential biomarker for peripheral arterial disease risk, future studies should ensure higher levels of training for adequate reproducibility.