bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of potential selective autophagy receptors from protein‐content profiling of autophagosomes
Authors: Cristiani Alberto , Dutta Arghya , Poveda‐Cuevas Sergio Alejandro , Kern Andreas , Bhaskara Ramachandra M. 
Published: April 2023

AbstractSelective autophagy receptors (SARs) are central to cellular homeostatic and organellar recycling pathways. Over the last two decades, more than 30 SARs have been discovered and validated using a variety of experimental approaches ranging from cell biology to biochemistry, including high‐throughput imaging and screening methods. Yet, the extent of selective autophagy pathways operating under various cellular contexts, for example, under basal and starvation conditions, remains unresolved. Currently, our knowledge of all known SARs and their associated cargo components is fragmentary and limited by experimental data with varying degrees of resolution. Here, we use classical predictive and modeling approaches to integrate high‐quality autophagosome content profiling data with disparate datasets. We identify a global set of potential SARs and their associated cargo components active under basal autophagy, starvation‐induced, and proteasome‐inhibition conditions. We provide a detailed account of cellular components, biochemical pathways, and molecular processes that are degraded via autophagy. Our analysis yields a catalog of new potential SARs that satisfy the characteristics of bonafide, well‐characterized SARs. We categorize them by the subcellular compartments they emerge from and classify them based on their likely mode of action. Our structural modeling validates a large subset of predicted interactions with the human ATG8 family of proteins and shows characteristic, conserved LC3‐interacting region (LIR)–LIR docking site (LDS) and ubiquitin‐interacting motif (UIM)–UIM docking site (UDS) binding modes. Our analysis also revealed the most abundant cargo molecules targeted by these new SARs. Our findings expand the repertoire of SARs and provide unprecedented details into the global autophagic state of HeLa cells. Taken together, our findings provide motivation for the design of new experiments, testing the role of these novel factors in selective autophagy.
Structure and function of the TPR‐domain immunophilins FKBP51 and FKBP52 in normal physiology and disease
Authors: Soto Olga B. , Ramirez Christian S. , Koyani Rina , Rodriguez‐Palomares Isela A. , Dirmeyer Jessica R. , Grajeda Brian , Roy Sourav , Cox Marc B. 
Published: April 2023

AbstractCoordinated cochaperone interactions with Hsp90 and associated client proteins are crucial for a multitude of signaling pathways in normal physiology, as well as in disease settings. Research on the molecular mechanisms regulated by the Hsp90 multiprotein complexes has demonstrated increasingly diverse roles for cochaperones throughout Hsp90‐regulated signaling pathways. Thus, the Hsp90‐associated cochaperones have emerged as attractive therapeutic targets in a wide variety of disease settings. The tetratricopeptide repeat (TPR)‐domain immunophilins FKBP51 and FKBP52 are of special interest among the Hsp90‐associated cochaperones given their Hsp90 client protein specificity, ubiquitous expression across tissues, and their increasingly important roles in neuronal signaling, intracellular calcium release, peptide bond isomerization, viral replication, steroid hormone receptor function, and cell proliferation to name a few. This review summarizes the current knowledge of the structure and molecular functions of TPR‐domain immunophilins FKBP51 and FKBP52, recent findings implicating these immunophilins in disease, and the therapeutic potential of targeting FKBP51 and FKBP52 for the treatment of disease.
DbMADS regulates carotenoid metabolism by repressing two carotenogenic genes in the green alga Dunaliella sp. FACHB‐847
Authors: Liang Ming‐Hua , Xie Shan‐Rong , Chen Hao‐Hong , Jiang Jian‐Guo 
Published: April 2023

AbstractMADS transcription factors are involved in the regulation of fruit development and carotenoid metabolism in plants. However, whether and how carotenoid accumulation is regulated by algal MADS are largely unknown. In this study, we first used functional complementation to confirm the functional activity of phytoene synthase from the lutein‐rich Dunaliella sp. FACHB‐847 (DbPSY), the key rate‐limiting enzyme in the carotenoid biosynthesis. Promoters of DbPSY and DbLcyB (lycopene β‐cyclase) possessed multiple cis‐acting elements such as light‐, UV‐B‐, dehydration‐, anaerobic‐, and salt‐responsive elements, W‐box, and C‐A‐rich‐G‐box (MADS‐box). Meanwhile, we isolated one nucleus‐localized MADS transcription factor (DbMADS), belonging to type I MADS gene. Three carotenogenic genes, DbPSY, DbLcyB, and DbBCH (β‐carotene hydroxylase) genes were upregulated at later stages, which was well correlated with the carotenoid accumulation. In contrast, DbMADS gene was highly expressed at lag phase with low carotenoid accumulation. Yeast one‐hybrid assay and dual‐luciferase reporter assay demonstrated that DbMADS could directly bind to the promoters of two carotenogenic genes, DbPSY and DbLcyB, and repress their transcriptions. This study suggested that DbMADS may act as a negative regulator of carotenoid biosynthesis by repressing DbPSY and DbLcyB at the lag phase, which provide new insights into the regulatory mechanisms of carotenoid metabolism in Dunaliella.
Targeting damaged collagen for intra‐articular delivery of therapeutics using collagen hybridizing peptides
Authors: Luke Emma N. , Ratnatilaka Na Bhuket Pahweenvaj , Yu Seungju M. , Weiss Jeffrey A. 
Published: April 2023

AbstractThe objective of this study was to investigate the potential of collagen hybridizing peptides (CHPs), which bind to denatured collagen, to extend the retention time of near‐infrared fluorophores (NIRF) following intra‐articular (IA) injection in rat knee joints. CHPs were synthesized with a NIRF conjugated to the N‐terminus. Male Sprague−Dawley rats were assigned to one of four experimental groups: healthy, CHP; osteoarthritis (OA), CHP; healthy, scrambled‐sequence CHP (sCHP), which has no collagen binding affinity; or OA, sCHP. Animals in the OA groups received an IA injection of monosodium iodoacetate to induce OA. All animals then received the corresponding CHP injection. Animals were imaged repeatedly over 2 weeks using an in vivo fluorescence imaging system. Joint components were isolated and imaged to determine CHP binding distribution. Safranin‐O and Fast Green histological staining was performed to confirm the development of OA. CHPs were found to be retained within the joint following IA injection in both healthy and OA animals for the full study period. In contrast, sCHP signal was negligible by 24−48 h. CHP signal was significantly greater (p < 0.05) in OA joints when compared to healthy joints. At the 2‐week end point, multiple joint components retained CHPs, including cartilage, meniscus, and synovium. CHPs dramatically extended the retention time of NIRFs following IA injection in healthy and OA knee joints by binding to multiple collagenous tissues in the joint. These results support the pursuit of further research to develop CHP based therapeutics for IA treatment of OA.
Timing and water temperature of drip irrigation regulate cotton growth and yield under film mulching in arid areas of Xinjiang
Authors: Wu Xiaodi , Wang Zhenhua , Guo Li , Liu Jian , Dhital Yam Prasad , Zhu Yan , Song Libing , Wen Yue 
Published: April 2023

AbstractBACKGROUNDCotton (Gossypium hirsutum L.) is the fiber crop most widely cultivated globally and one of the most important commercial crops in China, irrigation is closely related to the growth of cotton. A water temperature for irrigation that is too low or too high inhibits cotton growth. Poor irrigation timing results in water and nutrient deficiencies that reduce cotton yield. Therefore, it is necessary to determine the appropriate irrigation timing and water temperature.METHODWe conducted an experiment in an arid region of north‐western China to assess the effects of irrigation timing and water temperature on soil temperature and the photosynthetic characteristics, biomass, total nitrogen (N), and seed cotton yield. Two irrigation times (daytime and nighttime) and four water temperatures (15, 20, 25, and 30 °C) were combined into eight treatments.RESULTSOur results showed that water warming and nighttime irrigation improved the photosynthesis, biomass, N concentration (the proportion of total N weight in the plant biomass, in g kg−1), N content (the mass of total N, in g plant−1), and cotton yield. The optimal water temperature range for photosynthesis was 25.7–28.7 °C. Water warming also boosted the biomass allocation to the stem and increased the N allocation to the stem and leaf. Nighttime irrigation enhanced these phenomena. Water warming also increased the number of bolls per plant but reduced the single boll weight, increasing the seed cotton yield by 5.88–11.46%. At the same water temperature, irrigation during the night increased the number of bolls per plant and the single boll weight, improving the seed cotton yield by 2.95–4.31%. Among them, NI25 (nighttime irrigation with 25 °C water temperature) increased the yield by 14.13–14.90% compared with CK (daytime irrigation with 15 °C water temperature), which offers the best combination for increasing the yield.CONCLUSIONOur study clarifies the optimal irrigation timing and water temperature for cotton production under drip irrigation with film mulching, providing valuable information for improving the cotton yield in arid areas with temperate continental climate. © 2023 Society of Chemical Industry.
The Value of Multimodal Ultrasonic Scoring System in the Diagnosis of Carotid Vulnerable Plaque
Authors: Yan Lei , Ruan Qinyun , Ye Xiaojian , Xu Rongquan , Fu Liyun 
Published: April 2023

Background and AimsVulnerable plaques are closely related to ischemic stroke. To investigate the diagnostic value of multimodal plaque vulnerability ultrasound scoring system (PV‐USS) using histopathology as the gold standard.MethodsA total of 45 subjects who would be underwent carotid endarterectomy were recruited. The postoperative specimens were examined by histopathology. All responsible plaques were scanned dynamically in multiple sections by carotid ultrasound to measure maximum thickness and lumen stenotic degree, as well as, the echo, homogeneity, surface morphology, and echo type were observed. The above two‐dimensional (2D) ultrasonic features were systematically scored, that is, PV‐USS2D. Combined with contrast‐enhanced ultrasonography (CEUS), neovascularization grade in plaque was scored, which is PV‐USS2D+CEUS.ResultsAccording to the pathological results, 45 subjects were divided into vulnerable plaque group (27 cases, 60%) and non‐vulnerable plaque group (18 cases, 40%). PV‐USS2D and PV‐USS2D+CEUS in vulnerable plaque group were higher than those in non‐vulnerable plaque group (PV‐USS2D: 9.44 ± 2.10 vs 7.22 ± 1.73; PV‐USS2D+CEUS: 12.37 ± 2.10 vs 8.28 ± 1.81, P < .001). ROC curve analysis showed that the AUC of PV‐USS2D and PV‐USSCEUS was 0.783 and 0.929, respectively (P < .001). The best cutoff values of PV‐USS2D and PV‐USS2D+CEUS were, respectively, 9.5 (the maximum Youden index was 0.425, the sensitivity was 48.1%, the specificity was 94.4%) and 10.5 (the maximum Youden index was 0.667, the sensitivity was 77.8%, the specificity was 88.9%).ConclusionsUltrasound scoring system may be used as an effective method to evaluate the vulnerability of plaque. The diagnostic efficiency of PV‐USS2D+CEUS is more higher than PV‐USS2D.
Flash Nanoprecipitation Fabrication of PEI@Amorphous Calcium Carbonate Hybrid Nanoparticles for siRNA Delivery
Authors: Ren Qidi , Wang Lu , Qian Wenfei , Chen Baiqiu , Shuai Qi , Yan Yunfeng 
Published: April 2023

AbstractRNA interference (RNAi) is a promising approach for disease treatments. But the development of safe and effective delivery carriers remains a major challenge. Organic–inorganic hybrid nanoparticles (NPs), with the integration of functions from distinct materials, show great potential in small interfering RNA (siRNA) delivery. Herein, pH responsive amorphous calcium carbonate NPs (ACC NPs) are prepared using flash nanoprecipitation and hybrid NPs are constructed by coating ACC NPs with polyethyleneimine (PEI) for efficient siRNA delivery. PEI/ACC NPs show robust pH responsiveness and stability as well as effective siRNA loading and protection. Furthermore, siRNA‐loaded PEI/ACC NPs demonstrate enhanced cellular uptake and efficient endosomal escape, mediating improved siRNA delivery compared to pure PEI. These findings suggest that PEI/ACC NPs may have great potential in siRNA delivery for RNAi‐based therapy.
A 3D Bioprinted Nanoengineered Hydrogel with Photoactivated Drug Delivery for Tumor Apoptosis and Simultaneous Bone Regeneration via Macrophage Immunomodulation
Authors: Dutta Sayan Deb , Ganguly Keya , Hexiu Jin , Randhawa Aayushi , Moniruzzaman Md , Lim Ki‐Taek 
Published: April 2023

AbstractOne of the significant challenges in bone tissue engineering (BTE) is the healing of traumatic tissue defects owing to the recruitment of local infection and delayed angiogenesis. Herein, a 3D printable multi‐functional hydrogel composing polyphenolic carbon quantum dots (CQDs, 100 µg mL−1) and gelatin methacryloyl (GelMA, 12 wt%) is reported for robust angiogenesis, bone regeneration and anti‐tumor therapy. The CQDs are synthesized from a plant‐inspired bioactive molecule, 1, 3, 5‐trihydroxybenzene. The 3D printed GelMA‐CQDs hydrogels display typical shear‐thinning behavior with excellent printability. The fabricated hydrogel displayed M2 polarization of macrophage (Raw 264.7) cells via enhancing anti‐inflammatory genes (e.g., IL‐4 and IL10), and induced angiogenesis and osteogenesis of human bone mesenchymal stem cells (hBMSCs). The bioprinted hBMSCs are able to produce vessel‐like structures after 14 d of incubation. Furthermore, the 3D printed hydrogel scaffolds also show remarkable near infra‐red (NIR) responsive properties under 808 nm NIR light (1.0 W cm−2) irradiation with controlled release of antitumor drugs (≈49%) at pH 6.5, and thereby killing the osteosarcoma cells. Therefore, it is anticipated that the tissue regeneration and healing ability with therapeutic potential of the GelMA‐CQDs scaffolds may provide a promising alternative for traumatic tissue regeneration via augmenting angiogenesis and accelerated immunomodulation.
A circle‐to‐edge contact detection and resolution approach for beam‐particle modeling: cohesive materials and structural mechanics applications
Authors: Rima Aya , Oliver‐Leblond Cécile , Ragueneau Frédéric 
Published: April 2023

AbstractThis paper presents a new method for detecting contact between polygonal particles in the beam‐particle model. The main objective is to propose a robust and efficient algorithm capable of efficiently detecting contact between particles and increasing accuracy when complex particle shapes are used. This newly developed algorithm is based on a multi‐circle approach, where a set of circles is used to describe the shape of each particle. To validate and verify the algorithm, the developed approach is compared to the polygonal approach and to analytical results. For this purpose, several examples dealing with contact problems were performed. The obtained results show that the proposed contact detection procedure has the potential to efficiently detect the contact between two‐dimensional particles of complex shapes and provides a faster way to detect contact compared to the polygonal approach.
Analysis of dilatancy relation and shear‐band formation in granular materials based on Eshelby‐Mandel tensor
Authors: Guo Peijun , Zhou Shunhua , Stolle Dieter 
Published: April 2023

AbstractThe theory of configurational or material forces based on the Eshelby stress tensor (also called energy‐momentum tensor) has provided a general and efficient way to describe the motion of material defects and other inhomogeneities within the framework of continuum mechanics. In this paper, we explore how to use the configurational forces to describe the behavior of homogeneous granular materials by considering the material characteristics on both continuum and discrete particle levels. In particular, dissipative driving forces based on the Eshelby‐Mandel stress tensor are utilized as the driving force of the configuration variations in the form of shear‐induced volume change. The energy dissipation induced by the relative sliding at particle contacts is considered in the configurational forces. To characterize the dilation of a homogeneous granular material with uniform deformation, a virtual plane is introduced to facilitate the analysis and to derive the dilatancy formulation. With the consideration of the shear‐band geometry and the requirement of configurational force equilibrium across the boundary of a shear‐band, the condition for the onset of a shear band is derived. For granular specimens subjected to biaxial compression, the analyses recover the well‐known Rowe's dilatancy formulation and yield the shear‐band orientation identical to that obtained from the classical bifurcation analysis within the framework of elasto‐plasticity.
Regularized SPH model for soil–structure interaction with generalized frictional boundary
Authors: Wang Yadong , Wu Wei , Peng Chong 
Published: April 2023

AbstractThis paper proposes a regularized smoothed particle hydrodynamics (SPH) scheme to solve the problems of tensile instability and stress noise in large‐deformation soil–structure interaction. Particle shifting and stress regularization are combined to maintain uniform stresses and particle distributions. A generalized frictional boundary condition is presented to model soil–structure interfaces with abitrary friction coefficients. A modified particle shifting technique is developed to regularize particles near the frictional boundaries. Furthermore, GPU acceleration algorithm is adopted to improve the efficiency. The proposed scheme is compared with the conventional SPH methods using numerical examples, including the collapse of three‐dimensional granular column, the collapse of the cohesive soil, and pipe penetrates into soft clay. The comparison indicates that the proposed regularized SPH model can give highly accurate results for large‐deformation soil–structure interaction problems with arbitrary friction coefficient.
Weak correlation between total psoas muscle area and sarcopenia index for children with brain tumor
Authors: Wang Ziwen , Zeng Shuangmei , Liu Ling , Zhong Ximei , Cai Linbo 
Published: April 2023

AbstractObjectiveThe aim of this study is to determine whether the sarcopenia index (SI) is a viable measure of muscle mass in pediatric patients with brain tumors.MethodsRetrospectively enrolled patients (1–16 years) who had serum creatinine (Cr) and cystatin C (CysC) levels evaluated within 28 days of an abdomen magnetic resonance imaging scan for the lumbar vertebrae 3‐4 total psoas muscle area (tPMA) were studied. Variables were compared using their z scores calculated from age‐ and sex‐dependent reference. We hypothesized that a low SI indicated less skeletal muscle, and therefore potentially indicated sarcopenia.ResultsThe SI z score had no correlation with tPMA z score (r = 0.004). Both Cr and CysC levels were positively correlated with tPMA in z scores (r = 0.249 and 0.320). tPMA strongly correlated with body mass index in z scores (r = 0.582). The z scores of tPMA, Cr and CysC decreased with elevated World Health Organization grades of tumor, but the z scores of SI showed no significant dependence on WHO grades.ConclusionThe correlation of SI to muscle mass is very weak in our sample of pediatric patients with brain tumor. Its viability as biomarker for sarcopenia needs more study.
Patterns of Pharyngeal Obstruction and Collapse in Obese and Nonobese Children on Drug‐Induced Sleep Endoscopy
Authors: Sadiq Ibrahim , El‐Hakim Hamdy 
Published: April 2023

AbstractObjective(1) Compare proportions of collapse, obstruction, or mixed instances on drug‐induced sleep endoscopy findings of obese and nonobese children with obstructive sleep disordered breathing. (2) Determine the frequency of collapse in general between both groups.Study DesignRetrospective case‐control study.SettingTertiary pediatric center.MethodsObese (body mass index >95 percentile) children presenting with obstructive sleep disordered breathing (>33 on the pediatric sleep questionnaire) were identified from a prospectively kept surgical database. Only those who had undergone drug‐induced sleep endoscopy were eligible. Age and sex pair‐matched nonobese children were identified. Only nonsyndromic, neurologically normal, surgically naïve patients were included. The frequency of obstructive, collapse, and mixed pharyngeal patterns was documented in both groups. A comparison of proportions was then undertaken (χ2 test).ResultsOver a 5‐year period, 73 consecutive children with obesity were identified (40 males; mean of 8.5 ± 3.0 years, 2.8‐13.1). They were matched with 73 nonobese children (8.4 ± 3.0 years, 2.6‐14.1). The obese group exhibited significantly more pharyngeal collapses (62:47) (p = .0021 odds ratio [OR] 3.358, 95% confidence interval [CI] 1.52‐7.42). The proportion of pharyngeal findings on drug‐induced sleep endoscopy was significantly different (p = .000129) between the 2 groups; obese (61 mixed: 3 obstruction: 9 collapse) and nonobese (48 mixed: 22 obstruction: 4 collapse).ConclusionThe predominance of hypopharyngeal collapse in children with obesity may explain the likelihood of failure of surgery directed at obstructive findings. This may also strengthen the case for drug‐induced sleep endoscopy in this group at the initial surgery to guide it rather than after the failure of adenotonsillectomy.
Using acoustic tracking of an anadromous lamprey in a heavily fragmented river to assess current and historic passage opportunities and prioritise remediation
Authors: Jubb William M. , Noble Richard A. A. , Dodd Jamie R. , Nunn Andrew D. , Bolland Jonathan D. 
Published: April 2023

AbstractAnthropogenic structures extensively fragment riverine systems, reducing longitudinal connectivity, inhibiting migration and leading to severe declines in many fish populations, especially for diadromous species. This study investigated the upstream spawning migration of anadromous river lamprey (Lampetra fluviatilis) in a heavily fragmented tributary of the Humber Estuary, the location of one of the largest UK river lamprey populations. Overall, this study quantified river lamprey migration, spawning habitat distribution and historic river levels to develop a novel empirical index to understand the impact of man‐made barriers and prioritise their remediation. Passage at all weirs only occurred during episodic high river levels, often after prolonged delays with no lamprey passing below average levels for the time of year or utilising the fish pass at the first weir (T1) at the tidal limit. Barrier passage opportunities at the first four weirs were only possible for 30.3%, 38.7%, 52.1% and 6.7% of the migration period, but were lower and severely limited in 15 of the last 21 years. In addition, more lamprey (60%, n = 18) were last detected in reaches with no spawning habitat than in spawning habitat (40%, n = 12). Given the impassibility of, and lack of retreat from, T1 to other Humber tributaries, the River Trent is currently considered an ecological trap for a large proportion of lamprey that enter from the Humber Estuary. This passage should be urgently remediated, per the prioritisation index presented here, to aid river lamprey conservation, especially given their status as a designated feature of the Humber SAC.