bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-nucleus transcriptomics of IDH1- and TP53-mutant glioma stem cells displays diversified commitment on invasive cancer progenitors
Authors: Gulaia Valeriia , Shmelev Mikhail , Romanishin Aleksander , Shved Nikita , Farniev Vladislav , Goncharov Nikolay , Biktimirov Arthur , Vargas Irene Lisa , Khodosevich Konstantin , Kagansky Alexander , Kumeiko Vadim 
Published: November 2022

AbstractGlioma is a devastating brain tumor with a high mortality rate attributed to the glioma stem cells (GSCs) possessing high plasticity. Marker mutations in isocitrate dehydrogenase type 1 (IDH1) and tumor protein 53 (TP53) are frequent in gliomas and impact the cell fate decisions. Understanding the GSC heterogeneity within IDH1- and TP53- mutant tumors may elucidate possible treatment targets. Here, we performed single-nucleus transcriptomics of mutant and wild-type glioma samples sorted for Sox2 stem cell marker. For the first time the rare subpopulations of Sox2 + IDH1- and TP53-mutant GSCs were characterized. In general, GSCs contained the heterogeneity root subpopulation resembling active neural stem cells capable of asymmetric division to quiescent and transit amplifying cell branches. Specifically, double-mutant GSCs revealed the commitment on highly invasive oligodendrocyte- and astroglia-like progenitors. Additionally, double-mutant GSCs displayed upregulated markers of collagen synthesis, altered lipogenesis and high migration, while wild-type GSCs expressed genes related to ATP production. Wild-type GSC root population was highly heterogeneous and lacked the signature marker expression, thus glioblastoma treatment should emphasize on establishing differentiation protocol directed against residual GSCs. For the more differentiated IDH1- and TP53-mutant gliomas we suggest therapeutic targeting of migration molecules, such as CD44.
A new mode of luminescence in lanthanide oxalates metal–organic frameworks
Authors: Alzard Reem H. , Siddig Lamia A. , Saleh Na’il , Nguyen Ha L. , Nguyen Quynh Anh T. , Ho Thi H. , Bui Viet Q. , Sethupathi K. , Sreejith P. K. , Alzamly Ahmed 
Published: November 2022

AbstractTwo lanthanide metal–organic frameworks [Ln-MOFs, Ln = Eu(III), Tb(III)] composed of oxalic acid and Ln building units were hydrothermally synthesized and fully characterized by powder X-ray diffraction, Fourier-transform infrared spectroscopy, thermogravimetric analysis, scanning electron microscope, and energy-dispersive X-ray spectroscopy. Furthermore, their magnetic susceptibility measurements were obtained using SQUID based vibrating sample magnetometer (MPMS 3, Quantum Design). Both Ln-MOFs exhibited highly efficient luminescent property. Solid-state photoluminescence (PL) measurements revealed phosphorescence emission bands of Eu-MOF and Tb-MOF centered at 618 nm (red emission) and 550 nm (green emission) upon excitation at 396 nm and 285 nm, respectively. Eu-MOF and Tb-MOF displayed a phosphorescence quantum yield of 53% and 40%, respectively. Time-resolved PL analyses showed very long lifetime values, at 600 and 1065 ± 1 µs for Eu-MOF and Tb-MOF, respectively. Calculations performed by density functional theory indicated a charge transfer form metal centres to the ligand which was in good agreement with the experimental studies. Therefore, this new mode of highly photoluminescent MOF materials is studied for the first time which paves the way for better understanding of these systems for potential applications.
Identification of hub ferroptosis-related genes and immune infiltration in lupus nephritis using bioinformatics
Authors: Hu Weitao , Chen Xiaoqing 
Published: November 2022

AbstractLupus nephritis (LN) is one of the most severe and more common organ manifestations of the autoimmune disease, systemic lupus erythematosus. Ferroptosis, a novel type of programmed cell death, so far its role in LN remains uncertain. In the present study, we explored the role of ferroptosis in LN and its relationship with the immune response. The GSE112943 LN dataset was downloaded from the Gene Expression Omnibus database. Ferroptosis-Related Genes (FRGs) that drive, suppress or mark ferroptosis were retrieved from the public FerrDb database. The gene expression matrix of the GSE112943 dataset was analyzed with the “limma” package in R to obtain differentially expressed genes (DEGs) between LN and healthy samples. Subsequently, the crossover genes between DEGs and FRGs were identified as differentially expressed ferroptosis-related genes (DE-FRGs). Protein–protein interaction (PPI) network analysis, visualization, and identification of hub lupus nephritis ferroptosis-related genes (LN-FRGs) were performed with STRING and Cytoscape, while their Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were determined with the clusterProfiler package. Immune cell infiltration was calculated with CIBERSORT. The relationship between hub LN-FRGs and immune-infiltrated cells in LN was determined by Pearson correlation. A total of 96 DE-FRGs and 8 hub LN-FRGs (KRAS, PIK3CA, EGFR, MAPK14, SRC, MAPK3, VEGFA, and ATM) were identified. GO and KEGG functional classification indicated these genes enrichment in apoptotic process, programmed cell death, autophagy-animal, FoxO signaling pathway, relaxin signaling pathway, and VEGF signaling pathway. Infiltration matrix analysis of immune cells showed abundant Monocytes and M0/M1/M2 macrophages in LN kidney tissues. Correlation analysis revealed 8 hub LN-FRGs associated with immune-infiltrated cells in LN. In summary, overproduction of ROS and abnormal infiltration of immune cells would be implicated in the LN caused by ferroptosis. 8 hub lupus nephritis ferroptosis-related genes (LN-FRGs) which might be good biomarkers of ferroptosis in LN were identified in this study. These findings point to the immune response playing an important role in LN caused by ferroptosis via mutual regulation between hub LN-FRGs and immune-infiltrated cells.
Effect of anemoside B4 on milk whey in clinical mastitis-affected cows elucidated using tandem mass tag (TMT)-based quantitative proteomics
Authors: Shen Liu-hong , Zhang Yue , Shen Yu , Su Zhe-tong , Yu Shu-min , Cao Sui-zhong , Zong Xiao-lan 
Published: November 2022

AbstractIntramuscular injection of anemoside B4 (AB4) has a superior therapeutic effect on clinical mastitis in lactating cows. Here, we explored AB4’s effect on milk whey in clinical mastitis-affected cows using proteomics. Among fifty clinical mastitis cows received AB4 administration (0.05 ml/kg/day, for 7 days), twelve healed cows were selected and marked as group T. Twelve clinically heathy cows received the same dose of saline for 7 days, marked as group C. Collected milk whey of group T before and after AB4 administration marked as T1 and T2, respectively. The milk whey of group C after saline injection marked as C1. Milk whey protein changes were detected using tandem mass tag-based quantitative proteomic. We identified 872 quantifiable proteins in the samples. Among them, 511 proteins between T1 and C1, and 361 proteins between T2 and T1 were significantly altered. T1 than C1 had significantly more proteins associated with inflammatory damage and trans-endothelial migration of leukocytes, whereas these proteins were reduced in T2 treated with AB4. Compared with C, proteins associated with fibrin clot degradation and complement system activation were downregulated in T1 but upregulated in T2. In summary, AB4 can exert its therapeutic effect on clinical mastitis in cows mainly by reducing inflammatory damage, activating the complement system, inhibiting trans-endothelial migration of leukocytes, and promoting degradation of milk fibrin clots.
The negative impact of xenophobia on compassion with suffering out-group members is attenuated by trait empathy
Authors: Plieger Thomas , Marx Sophie , von Gagern Elena , Bode Stefan , Reuter Martin 
Published: November 2022

AbstractEmpathy enables human beings to understand and share the internal states of others. Studies show that empathy for pain is higher for in-group compared to out-group members. This might be driven by attitudes and biases towards out-groups. In a between subject design, N = 621 participants filled in questionnaires measuring xenophobia and trait empathy and were presented with photos of suffering individuals either from the in-group or an out-group, which had to be rated with respect to negative affect and the willingness to help the depicted persons. Results do not show more compassion with members of the in-group in general, but a negative effect of xenophobia on state empathy in the out-group condition. Additional moderation analyses show that this effect is less evident in presence of high trait empathy scores. Our results highlight the importance of empathy trainings to attenuate the effects of xenophobic attitudes on social cohabitation in our increasingly polarized and culturally diverse societies.
Using FlowCam and molecular techniques to assess the diversity of Cyanobacteria species in water used for food production
Authors: Mutoti Mulalo I. , Jideani Afam I. O. , Gumbo Jabulani R. 
Published: November 2022

AbstractGlobally, the occurrence of cyanobacteria in water currently remains an important subject as they produce cyanotoxins that pose threat to human health. Studies on the contamination of maize meals during mill grinding processes using cyanobacteria-contaminated water have not been conducted. The present study aimed to assess the diversity of cyanobacteria in the samples (process water, uncooked maize meal, and cooked maize meal (porridge)). Polymerized Chain Reaction (PCR) and Advanced digital flow cytometry (FlowCAM) were used to detect and identify cyanobacterial species available in these samples. 16S Primers (forward and reverse) tailed with Universal Sequences were used for amplification and sequencing of full-length 16S rRNA genes from cyanobacteria found in all samples. Cyanobacterial species from order Nostocales, Pseudanabaenales, Oscillatoriales Chroococcales, Synechococcales, and unclassified cyanobacterial order, some of which have the potential to produce cyanotoxins were amplified and identified in process water, raw maize meal and porridge samples using PCR. Images of the genusMicrocystis, Phormidium, andLeptolyngbyawere captured in process water samples using FlowCAM. These findings show the presence of cyanobacteria species in process water used for maize meal and the absence in cooked maize meal. The presence of cyanobacteria in process water is likely another route of human exposure to cyanotoxins.
Three-dimensional mapping reveals heterochronic development of the neuromuscular system in postnatal mouse skeletal muscles
Authors: Xu Jianyi , Zhu Jingtan , Li Yusha , Yao Yingtao , Xuan Ang , Li Dongyu , Yu Tingting , Zhu Dan 
Published: November 2022

AbstractThe development of the neuromuscular system, including muscle growth and intramuscular neural development, in addition to central nervous system maturation, determines motor ability improvement. Motor development occurs asynchronously from cephalic to caudal. However, whether the structural development of different muscles is heterochronic is unclear. Here, based on the characteristics of motor behavior in postnatal mice, we examined the 3D structural features of the neuromuscular system in different muscles by combining tissue clearing with optical imaging techniques. Quantitative analyses of the structural data and related mRNA expression revealed that there was continued myofiber hyperplasia of the forelimb and hindlimb muscles until around postnatal day 3 (P3) and P6, respectively, as well as continued axonal arborization and neuromuscular junction formation until around P3 and P9, respectively; feature alterations of the cervical muscle ended at birth. Such structural heterochrony of muscles in different body parts corresponds to their motor function. Structural data on the neuromuscular system of neonatal muscles provide a 3D perspective in the understanding of the structural status during motor development.
Matching amino acids membrane preference profile to improve activity of antimicrobial peptides
Authors: Kim Shanghyeon , Lee Jaehoo , Lee Sol , Kim Hyein , Sim Ji-Yeong , Pak Boryeong , Kim Kyeongmin , Il Kim Jae 
Published: November 2022

AbstractAntimicrobial peptides (AMPs) are cationic antibiotics that can kill multidrug-resistant bacteria via membrane insertion. However, their weak activity limits their clinical use. Ironically, the cationic charge of AMPs is essential for membrane binding, but it obstructs membrane insertion. In this study, we postulate that this problem can be overcome by locating cationic amino acids at the energetically preferred membrane surface. All amino acids have an energetically preferred or less preferred membrane position profile, and this profile is strongly related to membrane insertion. However, most AMPs do not follow this profile. One exception is protegrin-1, a powerful but neglected AMP. In the present study, we found that a potent AMP, WCopW5, strongly resembles protegrin-1 and that the match between its sequence and the preferred position profile closely correlates with its antimicrobial activity. One of its derivatives, WCopW43, has antimicrobial activity comparable to that of the most effective AMPs in clinical use.
Structure-guided product determination of the bacterial type II diterpene synthase Tpn2
Authors: Stowell Emma A. , Ehrenberger Michelle A. , Lin Ya-Lin , Chang Chin-Yuan , Rudolf Jeffrey D. 
Published: November 2022

AbstractA grand challenge in terpene synthase (TS) enzymology is the ability to predict function from protein sequence. Given the limited number of characterized bacterial TSs and significant sequence diversities between them and their eukaryotic counterparts, this is currently impossible. To contribute towards understanding the sequence-structure-function relationships of type II bacterial TSs, we determined the structure of the terpentedienyl diphosphate synthase Tpn2 fromKitasatosporasp. CB02891 by X-ray crystallography and made structure-guided mutants to probe its mechanism. Substitution of a glycine into a basic residue changed the product preference from the clerodane skeleton to asyn-labdane skeleton, resulting in the firstsyn-labdane identified from a bacterial TS. Understanding how a single residue can dictate the cyclization pattern in Tpn2, along with detailed bioinformatics analysis of bacterial type II TSs, sets the stage for the investigation of the functional scope of bacterial type II TSs and the discovery of novel bacterial terpenoids.
Unbounded randomness from uncharacterized sources
Authors: Avesani Marco , Tebyanian Hamid , Villoresi Paolo , Vallone Giuseppe 
Published: November 2022

AbstractRandomness is a central feature of quantum mechanics and an invaluable resource for both classical and quantum technologies. Commonly, in Device-Independent and Semi-Device-Independent scenarios, randomness is certified using projective measurements, and its amount is bounded by the quantum system’s dimension. Here, we propose a Source-Device-Independent protocol, based on Positive Operator Valued Measurement (POVM), which can arbitrarily increase the number of certified bits for any fixed dimension. Additionally, the proposed protocol doesn’t require an initial seed and active basis switching, simplifying its experimental implementation and increasing the generation rates. A tight lower-bound on the quantum conditional min-entropy is derived using only the POVM structure and the experimental expectation values, taking into account the quantum side-information. For symmetric POVM on the Bloch sphere, we derive closed-form analytical bounds. Finally, we experimentally demonstrate our method with a compact and simple photonic setup that employs polarization-encoded qubits and POVM up to 6 outcomes.
Interaction of microswimmers in viscoelastic liquid crystals
Authors: Chi Hai , Gavrikov Alexander , Berlyand Leonid , Aranson Igor S. 
Published: November 2022

AbstractSwimming bacteria successfully colonize complex non-Newtonian environments exemplified by viscoelastic media and liquid crystals. While there is a significant body of research on microswimmer motility in viscoelastic liquids, the motion in anisotropic fluids still lacks clarity. This paper studies how individual microswimmers (e.g., bacteria) interact in a mucus-like environment modeled by a visco-elastic liquid crystal. We have found that an individual swimmer moves faster along the same track after the direction reversal, in faithful agreement with the experiment. This behavior is attributed to the formation of the transient tunnel due to the visco-elastic medium memory. We observed that the aft swimmer has a higher velocity for two swimmers traveling along the same track and catches up with the leading swimmer. Swimmers moving in a parallel course attract each other and then travel at a close distance. A pair of swimmers launched at different angles form a "train”: after some transient, the following swimmers repeat the path of the "leader”. Our results shed light on bacteria penetration in mucus and colonization of heterogeneous liquid environments.
Simplicial cascades are orchestrated by the multidimensional geometry of neuronal complexes
Authors: Kilic Bengier Ülgen , Taylor Dane 
Published: November 2022

AbstractCascades over networks (e.g., neuronal avalanches, social contagions, and system failures) often involve higher-order dependencies, yet theory development has largely focused on pairwise-interaction models. Here, we develop a ‘simplicial threshold model’ (STM) for cascades over simplicial complexes that encode dyadic, triadic and higher-order interactions. Focusing on small-world models containing both short- and long-range k-simplices, we explore spatio-temporal patterns that manifest as a frustration between local and nonlocal propagations. We show that higher-order interactions and nonlinear thresholding coordinate to robustly guide cascades along a k-dimensional generalization of paths that we call ‘geometrical channels’. We also find this coordination to enhance the diversity and efficiency of cascades over a simplicial-complex model for a neuronal network, or ‘neuronal complex’. We support these findings with bifurcation theory and data-driven approaches based on latent geometry. Our findings provide fruitful directions for uncovering the multiscale, multidimensional mechanisms that orchestrate the spatio-temporal patterns of nonlinear cascades.
What Is Clinical Evidence in Speech-Language Pathology? A Scoping Review
Authors: Fissel Brannick Schea , Wolford George W. , Wolford Laura L. , Effron Kayleigh , Buckler Jennifer 
Published: November 2022

Purpose:

Two disparate models drive American speech-language pathologists' views of evidence-based practice (EBP): the American Speech-Language-Hearing Association's (2004a, 2004b) and Dollaghan's (2007). These models discuss evidence derived from clinical practice but differ in the terms used, the definitions, and discussions of its role. These concepts, which we unify as
clinical evidence
, are an important part of EBP but lack consistent terminology and clear definitions in the literature. Our objective was to identify how clinical evidence is described in the field.

Method:
We conducted a scoping review to identify terms ascribed to clinical evidence and their descriptions. We searched the peer-reviewed, accessible, speech-language pathology intervention literature from 2005 to 2020. We extracted the terms and descriptions, from which three types of clinical evidence arose. We then used an open-coding framework to categorize positive and negative descriptions of clinical expertise and summarize the role of clinical evidence in decision making.

Results:

Seventy-eight articles included a description of clinical evidence. Across publications, a single term was used to describe disparate concepts, and the same concept was given different terms, yet the concepts that authors described clustered into three categories:
clinical opinion, clinical expertise,
and
practice-based evidence,
with each described as distinct from research evidence, and separate from the process of clinical decision making. Clinical opinion and clinical expertise were intrinsic to the clinician. Clinical opinion was insufficient and biased, whereas clinical expertise was a positive multidimensional construct. Practice-based evidence was extrinsic to the clinician—the local clinical data that clinicians generated. Good clinical decisions integrated multiple sources of evidence.

Conclusions:
These results outline a shared language for SLPs to discuss their clinical evidence with researchers, families, allied professionals, and each other. Clarification of the terminology, associated definitions, and the contributions of clinical evidence to good clinical decision-making informs EBP models in speech-language pathology.

Supplemental Material:

https://doi.org/10.23641/asha.21498546
A bi‐layer stochastic coordinated planning framework for wind‐battery power systems considering bilateral carbon trading
Authors: Nan Junpei , Feng Jieran , Deng Xu , Wang Chao , Sun Ke , Zhou Hao 
Published: November 2022

AbstractRenewable energy and energy storage are essential technologies for decarbonizing energy systems. Expansion planning of the two technologies considering source‐side carbon responsibility has been well studied. However, expansion planning considering both source‐side and load‐side carbon responsibility, which may simultaneously stimulate the carbon reduction potential of source and load, has been rarely studied. To fill this research gap, this paper proposes a bi‐layer wind turbine generator (WTG) and demand‐side battery (DSB) coordinated planning framework considering wind power and load uncertainties. Moreover, a novel source‐load bilateral carbon trading (BCT) mechanism based on the Aumann–Shapley method is proposed to stimulate the WTG and DSB configuration. In the bi‐layer planning framework with BCT mechanism, WTG and DSB capacity planning with the two‐stage stochastic optimization are conducted in the upper and lower layer, respectively. Finally, test results on a modified IEEE 24‐bus system demonstrate that the proposed framework with BCT mechanism can effectively motivate the planning configuration of WTG and DSB and carbon mitigation. Compared with the models with unilateral carbon trading mechanisms, the proposed model has advantages in stimulating configuration of WTG and DSB, reducing carbon emissions, and balancing source‐load economic burden from carbon trading.
High conversion ratio buck–boost DC–DC converter based on coupled inductor
Authors: Alizadeh Darioush , Babaei Ebrahim , Mousavi S.M.J. 
Published: November 2022

AbstractHere, a buck–boost DC–DC converter based on coupled inductor is proposed. At first, the proposed converter's operation modes and theoretical relations are reviewed and analyzed. Then, to operate the proposed converter in continuous conduction mode (CCM), the optimal value of the elements is designed. Then, the comparison results are presented to highlight the advantages and disadvantages of the proposed converter. The proposed DC–DC converter has benefits such as high conversion ratio capability, continuous input current, common ground, and low voltage stress on elements. Finally, the experimental results of the proposed converter's prototype are presented for both buck and boost operations to confirm the theoretical relations and verify the claims made.