bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photobiomodulation inhibits the activation of neurotoxic microglia and astrocytes by inhibiting Lcn2/JAK2-STAT3 crosstalk after spinal cord injury in male rats
Authors: Wang Xuankang , Li Xin , Zuo Xiaoshuang , Liang Zhuowen , Ding Tan , Li Kun , Ma Yangguang , Li Penghui , Zhu Zhijie , Ju Cheng , Zhang Zhihao , Song Zhiwen , Quan Huilin , Zhang Jiawei , Hu Xueyu , Wang Zhe 
Published: November 2021

Abstract
Background
Neurotoxic microglia and astrocytes begin to activate and participate in pathological processes after spinal cord injury (SCI), subsequently causing severe secondary damage and affecting tissue repair. We have previously reported that photobiomodulation (PBM) can promote functional recovery by reducing neuroinflammation after SCI, but little is known about the underlying mechanism. Therefore, we aimed to investigate whether PBM ameliorates neuroinflammation by modulating the activation of microglia and astrocytes after SCI.

Methods
Male Sprague–Dawley rats were randomly divided into three groups: a sham control group, an SCI + vehicle group and an SCI + PBM group. PBM was performed for two consecutive weeks after clip-compression SCI models were established. The activation of neurotoxic microglia and astrocytes, the level of tissue apoptosis, the number of motor neurons and the recovery of motor function were evaluated at different days post-injury (1, 3, 7, 14, and 28 days post-injury, dpi). Lipocalin 2 (Lcn2) and Janus kinase-2 (JAK2)-signal transducer and activator of transcription-3 (STAT3) signaling were regarded as potential targets by which PBM affected neurotoxic microglia and astrocytes. In in vitro experiments, primary microglia and astrocytes were irradiated with PBM and cotreated with cucurbitacin I (a JAK2-STAT3 pathway inhibitor), an adenovirus (shRNA-Lcn2) and recombinant Lcn2 protein.

Results
PBM promoted the recovery of motor function, inhibited the activation of neurotoxic microglia and astrocytes, alleviated neuroinflammation and tissue apoptosis, and increased the number of neurons retained after SCI. The upregulation of Lcn2 and the activation of the JAK2-STAT3 pathway after SCI were suppressed by PBM. In vitro experiments also showed that Lcn2 and JAK2-STAT3 were mutually promoted and that PBM interfered with this interaction, inhibiting the activation of microglia and astrocytes.

Conclusion
Lcn2/JAK2-STAT3 crosstalk is involved in the activation of neurotoxic microglia and astrocytes after SCI, and this process can be suppressed by PBM.
Hyaluronic acid hydrogel encapsulated BMP-14-modified ADSCs accelerate cartilage defect repair in rabbits
Authors: Liu Hao , Rui Yongjun , Liu Jun , Gao Fandong , Jin Yesheng 
Published: November 2021

Abstract
Background
Cartilage defect has a limited capacity to heal. In this context, we hypothesized that hyaluronic acid (HA) hydrogel encapsulated BMP-14-modified adipose-derived mesenchymal stem cells (ADSCs) could accelerate cartilage defect repair in rabbits.

Methods
ADSCs were isolated and identified by flow cytometry. ADSCs were treated with adenovirus vector encoding BMP-14 (Ad-BMP-14) or adenovirus vector encoding control (Ad-ctrl). Real-time PCR (RT-PCR) and western blot assay was performed to verify the transfection efficacy and chondrogenic differentiation markers (ACAN, Collagen II and SOX9). Rabbit cartilage defect model was performed and randomly divided into following groups: control group, HA hydrogel + ADSCs, ADSCs, HA hydrogel + Lv-ctrl-ADSCs, HA hydrogel + BMP-14 transfected ADSCs. At 6, 9 and 12 weeks after surgery, scanning electron microscopy, hematoxylin–eosin, Safranin-O/Fast Green and immunohistochemical staining for Collagen II were performed to determine the role of HA hydrogel encapsulated BMP-14-modified ADSCs in cartilage repair in vivo.

Results
ADSCs were successfully isolated and positively expressed CD29, CD44 and CD90. Transfection efficacy of Ad-BMP-14 was verified by RT-PCR and western blot assay. Moreover, Ad-BMP-14 could significantly increased chondrogenic differentiation markers (ACAN, Collagen II and SOX9). The LV-BMP-14-ADSCs and HA hydrogel + LV-BMP-14-ADSCs groups revealed smoother surface cartilage repair that was level with the surrounding cartilage and almost complete border integration.

Conclusions
HA hydrogel encapsulated BMP-14-modified ADSCs accelerate cartilage defect repair in rabbits. We need to further validate the specific mechanism of action of HA hydrogel encapsulated LV-BMP-14-ADSCs involved in the repairing cartilage damage in vivo.
Parkinson's in the bone
Authors: Xiong Lei , Pan Jin-Xiu , Guo Hao-han , Mei Lin , Xiong Wen-Cheng 
Published: November 2021

AbstractPatients with Parkinson’s disease (PD) exhibit systemic deficits, including arthritis and osteoporosis-like symptoms. However, the questions, how the deficits in periphery organs or tissues occur in PD patients, and what are the relationship (s) of the periphery tissue deficits with the brain pathology (e.g., dopamine neuron loss), are at the beginning stage to be investigated. Notice that both PD and osteoporosis are the products of a complex interaction of genetic and environmental risk factors. Genetic mutations in numerous genes have been identified in patients either with recessive or autosomal dominant PD. Most of these PD risk genes are ubiquitously expressed; and many of them are involved in regulation of bone metabolism. Here, we review the functions of the PD risk genes in regulating bone remodeling and homeostasis. The knowledge gaps in our understanding of the bone-to-brain axis in PD development are also outlined.
The protective effect of Jangkanghwan (Korean traditional food) on lipopolysaccharide-induced disruption of the colonic epithelial barrier
Authors: Long Xingyao , Kim Yong-kyu , Yu Ting , Yi Ruokun , Zhao Xin , Park Kun-young 
Published: November 2021

AbstractJangkanghwan (JKH) is a Korean traditional food that is a mixture of food ingredients and traditional Korean medicine ingredients, and it has been observed to produce satisfactory anti-inflammatory, antioxidant, and antibacterial effects. In the current study, JKH was administered by gavage to BALB/C mice with lipopolysaccharide (LPS)-induced colonic epithelial dysfunction, and mouse body weight and food intake were recorded. Indexes such as colonic paracellular permeability, serum inflammatory cytokines, and bacterial translocation were used to comprehensively evaluate the regulatory effect of JKH on mouse colonic epithelial function, and qPCR and Western blot were also used to analyze the expression of tight junction (TJ)-related genes, such as occludin, claudin, zonula occludens (ZOs) proteins, and junction adhesion molecules (JAM) in the colonic epithelial tissue. The experimental results indicated that JKH relieved the edema of the liver, spleen, and mesenteric lymph node tissues, and reduced the loss of appetite and diarrhea caused by LPS injection in mice. It increased the amount of mice food intake from 3.7 g/day in the LPS group to 4.7 g per day; the water content in the feces of mice in the JKH group was 13.86% less than that in the LPS group. JKH reduced the inflammatory response in mice caused by LPS, protected the integrity of the colon, the permeability of fluorescent macromolecules was one-fourth of the LPS group, and enhanced the mRNA and protein expression of TJ-related proteins in colon tissue. Our findings highlight that JKH has benefits in intestinal health and relieving systemic inflammation, relevant aspects of its use as a functional food.
Enhancement on antioxidant and antibacterial activities of Brightwell blueberry by extraction and purification
Authors: Liu Haonan , Wu Han , Wang Ying , Wang Fan , Liu Xiaoli , Zhou Jianzhong 
Published: November 2021

AbstractA blueberry anthocyanin extract was obtained from Brightwell blueberry fruits cultivated in eastern China and the extraction and purification conditions were optimized. The components of the anthocyanin extract were identified using ultra-performance liquid chromatography-electrospray ionization interface-mass spectrometer. The antioxidant and antibacterial activities of the blueberry fruit supernatant (BFS), blueberry anthocyanin crude extract (BCE), and blueberry anthocyanin rich extract (BRE) were evaluated. The extraction yield was 1.79 ± 0.0014 mg/g under the following optimal conditions: 1:20 solid-to-liquid ratio (v/w), 24 h, 34 °C, and 90% ethanol containing 0.21% (v/v) hydrochloric acid. With regard to purification, anthocyanin purity increased 19.1-fold. Nine fractions were identified as the glycosides of delphinidin, cyanidin, petunidin, and malvidin. The biological activities of the blueberry anthocyanin extract were improved through extraction and purification. Compared with BFS and BCE, BRE had a higher DPPH radical scavenging activity (EC50 = 0.51 mg/mL), ABTS antioxidant capacity (EC50 = 0.32 mg/mL), and oxygen radical absorbance capacity (0.43 mmol Trolox/g). Furthermore, BRE (2 mg/mL) showed a maximum of 84.64 ± 0.35% reduction in the biofilm biomass of Listeria monocytogenes and the inhibition zone given by BRE against Escherichia coli was 16.04 ± 0.38 mm. BRE showed the highest antioxidant capacities and obvious antibacterial effects against food-related microorganisms than the other samples. Therefore, BRE can be used as a natural antioxidant and antibacterial agent and has potential health advantages and food industry applications.
Metabolic engineering strategies for de novo biosynthesis of sterols and steroids in yeast
Authors: Gu Yuehao , Jiao Xue , Ye Lidan , Yu Hongwei 
Published: November 2021

AbstractSteroidal compounds are of great interest in the pharmaceutical field, with steroidal drugs as the second largest category of medicine in the world. Advances in synthetic biology and metabolic engineering have enabled de novo biosynthesis of sterols and steroids in yeast, which is a green and safe production route for these valuable steroidal compounds. In this review, we summarize the metabolic engineering strategies developed and employed for improving the de novo biosynthesis of sterols and steroids in yeast based on the regulation mechanisms, and introduce the recent progresses in de novo synthesis of some typical sterols and steroids in yeast. The remaining challenges and future perspectives are also discussed.
Classifying the tracing difficulty of 3D neuron image blocks based on deep learning
Authors: Yang Bin , Huang Jiajin , Wu Gaowei , Yang Jian 
Published: November 2021

AbstractQuickly and accurately tracing neuronal morphologies in large-scale volumetric microscopy data is a very challenging task. Most automatic algorithms for tracing multi-neuron in a whole brain are designed under the Ultra-Tracer framework, which begins the tracing of a neuron from its soma and traces all signals via a block-by-block strategy. Some neuron image blocks are easy for tracing and their automatic reconstructions are very accurate, and some others are difficult and their automatic reconstructions are inaccurate or incomplete. The former are called low Tracing Difficulty Blocks (low-TDBs), while the latter are called high Tracing Difficulty Blocks (high-TDBs). We design a model named 3D-SSM to classify the tracing difficulty of 3D neuron image blocks, which is based on 3D Residual neural Network (3D-ResNet), Fully Connected Neural Network (FCNN) and Long Short-Term Memory network (LSTM). 3D-SSM contains three modules: Structure Feature Extraction (SFE), Sequence Information Extraction (SIE) and Model Fusion (MF). SFE utilizes a 3D-ResNet and a FCNN to extract two kinds of features in 3D image blocks and their corresponding automatic reconstruction blocks. SIE uses two LSTMs to learn sequence information hidden in 3D image blocks. MF adopts a concatenation operation and a FCNN to combine outputs from SIE. 3D-SSM can be used as a stop condition of an automatic tracing algorithm in the Ultra-Tracer framework. With its help, neuronal signals in low-TDBs can be traced by the automatic algorithm and in high-TDBs may be reconstructed by annotators. 12732 training samples and 5342 test samples are constructed on neuron images of a whole mouse brain. The 3D-SSM achieves classification accuracy rates 87.04% on the training set and 84.07% on the test set. Furthermore, the trained 3D-SSM is tested on samples from another whole mouse brain and its accuracy rate is 83.21%.
Monocytic THP-1 cells diverge significantly from their primary counterparts: a comparative examination of the chromosomal conformations and transcriptomes
Authors: Liu Yulong , Li Hua , Czajkowsky Daniel M. , Shao Zhifeng 
Published: November 2021

AbstractImmortalized cell lines have long been used as model systems to systematically investigate biological processes under controlled and reproducible conditions, providing insights that have greatly advanced cellular biology and medical sciences. Recently, the widely used monocytic leukemia cell line, THP-1, was comprehensively examined to understand mechanistic relationships between the 3D chromatin structure and transcription during the trans-differentiation of monocytes to macrophages. To corroborate these observations in primary cells, we analyze in situ Hi-C and RNA-seq data of human primary monocytes and their differentiated macrophages in comparison to that obtained from the monocytic/macrophagic THP-1 cells. Surprisingly, we find significant differences between the primary cells and the THP-1 cells at all levels of chromatin structure, from loops to topologically associated domains to compartments. Importantly, the compartment-level differences correlate significantly with transcription: those genes that are in A-compartments in the primary cells but are in B-compartments in the THP-1 cells exhibit a higher level of expression in the primary cells than in the THP-1 cells, and vice versa. Overall, the genes in these different compartments are enriched for a wide range of pathways, and, at least in the case of the monocytic cells, their altered expression in certain pathways in the THP-1 cells argues for a less immune cell-like phenotype, suggesting that immortalization or prolonged culturing of THP-1 caused a divergence of these cells from their primary counterparts. It is thus essential to reexamine phenotypic details observed in cell lines with their primary counterparts so as to ensure a proper understanding of functional cell states in vivo.
Functional analysis of enhancer elements regulating the expression of the Drosophila homeodomain transcription factor DRx by gene targeting
Authors: Klöppel Christine , Hildebrandt Kirsten , Kolb Dieter , Fürst Nora , Bley Isabelle , Karlowatz Ruth-Jessica , Walldorf Uwe 
Published: November 2021

AbstractBackgroundTheDrosophilabrain is an ideal model system to study stem cells, here called neuroblasts, and the generation of neural lineages. Many transcriptional activators are involved in formation of the brain during the development ofDrosophila melanogaster. The transcription factorDrosophilaRetinal homeobox (DRx), a member of the 57B homeobox gene cluster, is also one of these factors for brain development.ResultsIn this study a detailed expression analysis of DRx in different developmental stages was conducted. We show that DRx is expressed in the embryonic brain in the protocerebrum, in the larval brain in the DM and DL lineages, the medulla and the lobula complex and in the central complex of the adult brain. We generated a DRx enhancer trap strain by gene targeting and reintegration of Gal4, which mimics the endogenous expression of DRx. With the help of eight existing enhancer-Gal4 strains and one made by our group, we mapped various enhancers necessary for the expression of DRx during all stages of brain development from the embryo to the adult. We made an analysis of some larger enhancer regions by gene targeting. Deletion of three of these enhancers showing the most prominent expression patterns in the brain resulted in specific temporal and spatial loss of DRx expression in defined brain structures.ConclusionOur data show that DRx is expressed in specific neuroblasts and defined neural lineages and suggest that DRx is another important factor forDrosophilabrain development.
Travelers’ attitude towards carpooling in Islamabad
Authors: Ayaz Altaf , Waheed Abdul , Saleem Hamza , Abid Malik Muneeb 
Published: November 2021

AbstractIslamabad, being the capital of Pakistan, is attracting every business. Thus, the city is growing towards traffic congestion as the city’s car ownership rate is rapidly growing. In such a situation, for successful implementation, the policymakers need to understand the public acceptance of carpooling services based on its key motives and constraints. This research explores the key motives and constraints to the introduction scenarios of carpooling service in Islamabad. A stated preference questionnaire survey was conducted via Google Form comprising several parts relating to carpooling. Exploratory and confirmatory factor analyses were processed, and a structural model was developed. Females (both single and married) were less orientated to carpool with males and married males with females. Unknown carpooling partners negatively influenced the factor of intention to shift to carpooling service. Our study provides policymakers and transport planners with an appropriate forecasting model of significant factors. In addition, it provides suggestions to transport planners to design promotional tools to enhance the tendency of carpooling among private car users in favor of reducing traffic congestion and increased car ownership rate in the city.
Effects of Lorentz violation in superconductivity
Authors: Furtado J. , Costa Filho R. M. M. , Morais A. F. , Jardim I. C. 
Published: November 2021

Abstract
This paper presents the effects of Lorentz violation in superconductivity. Constructing a Lorentz-violating Ginzburg-Landau theory of superconductivity we discuss the influence of the Lorentz-violating tensors

and

in London's penetration depth, in the coherence length and critical magnetic field.
Deep learning is widely applicable to phenotyping embryonic development and disease
Authors: Naert Thomas , Çiçek Özgün , Ogar Paulina , Bürgi Max , Shaidani Nikko-Ideen , Kaminski Michael M. , Xu Yuxiao , Grand Kelli , Vujanovic Marko , Prata Daniel , Hildebrandt Friedhelm , Brox Thomas , Ronneberger Olaf , Voigt Fabian F. , Helmchen Fritjof , Loffing Johannes , Horb Marko E. , Willsey Helen Rankin , Lienkamp Soeren S. 
Published: November 2021

ABSTRACT
Genome editing simplifies the generation of new animal models for congenital disorders. However, the detailed and unbiased phenotypic assessment of altered embryonic development remains a challenge. Here, we explore how deep learning (U-Net) can automate segmentation tasks in various imaging modalities, and we quantify phenotypes of altered renal, neural and craniofacial development in Xenopus embryos in comparison with normal variability. We demonstrate the utility of this approach in embryos with polycystic kidneys (pkd1 and pkd2) and craniofacial dysmorphia (six1). We highlight how in toto light-sheet microscopy facilitates accurate reconstruction of brain and craniofacial structures within X. tropicalis embryos upon dyrk1a and six1 loss of function or treatment with retinoic acid inhibitors. These tools increase the sensitivity and throughput of evaluating developmental malformations caused by chemical or genetic disruption. Furthermore, we provide a library of pre-trained networks and detailed instructions for applying deep learning to the reader's own datasets. We demonstrate the versatility, precision and scalability of deep neural network phenotyping on embryonic disease models. By combining light-sheet microscopy and deep learning, we provide a framework for higher-throughput characterization of embryonic model organisms.
This article has an associated ‘The people behind the papers’ interview.
Photophoretic asymmetry factors for an absorptive dielectric cylinder near a reflecting planar boundary
Authors: Mitri F. G. 
Published: November 2021

The effect of a perfectly reflecting boundary (i.e., planar wall) on the photophoretic asymmetry factors (PAFs) for an absorptive dielectric cylinder is investigated. The expression for the normalized intensity function for the electric field internal to the cylinder is used in conjunction with the multiple scattering theory of waves, the translational addition theorem in cylindrical coordinates, and the method of images to derive analytically and compute numerically the longitudinal (L) and transverse (T) PAFs for the cylinder as well as the internal dimensionless intensity function. Both TM- and TE-polarized plane progressive waves with arbitrary incidence (in the polar plane) are considered. Particular emphases are given on the dimensionless size parameter of the cylinder, the incidence angle of the illuminating field, and the dimensionless distance parameter from the flat surface. The results show that the net effect of the planar wall increases or decreases the amplitudes of the PAFs (thus, the photophoretic force and torque), depending on the particle-wall distance, incidence angle, particle size, and the polarization of the incident field. The results of this analysis are useful in applications related to electromagnetic/optical scattering, particle manipulations, optically bound matter, and photophoresis.
A qualitative study to understand drivers of psychoactive substance use among Nepalese youth
Authors: Bhandari Tulsi Ram , Khatiwada Bhushan , Rajbhandari Bibika , Bestman Amy , Mistry Sabuj Kanti , Rayamajhee Binod , Rawal Lal B. , Yadav Uday Narayan 
Published: November 2021

Background
Psychoactive substance use among youth is an emerging public health issue in Nepal. This exploratory study aimed to better understand the drivers of psychoactive substance use among Nepalese youth in Rupandehi district of Nepal.

Materials and methods
This study used a qualitative approach for data collection. Both in-depth interviews (IDI, seven participants) and focus group discussions (FGD, 13 participants) were conducted among study participants who self-reported as psychoactive substance users or had history of psychoactive substance use. Participants for IDI were aged between 11 and 24 years and between 18 and 35 years old for FGDs. Semi-structured interview guides were prepared separately for IDIs and FDGs. Interviews were conducted in Nepali language and were audio recorded, which were there transcribed and translated into English for coding and analyses. In addition, interviews notes were taken by two research assistants. An inductive thematic analysis was used to analyze the data.

Results
This study identified a range of drivers of psychoactive substances use among Nepalese youths. Themes included (i) socio-cultural factors, (ii) individual factors, (iii) academic environment, (iv) physical environment and the (v) influence of media. The socio-cultural factors were categorized into sub-themes of family relationships, ethnic identity and psychoactive substance use and lack of social acceptance. Individual factors included peer pressure, stress relief and coping with financial challenges. Accessibility and availability of psychoactive substances in the surrounding environment and lack of monitoring and reinforcement of rules/ law and regulations were other drivers to psychoactive substance use among this Nepalese youth cohort.

Conclusion
Our study identified several important drivers of psychoactive substance use among youth in the Rupandehi district of Nepal. Future works are anticipated to further explore youth initiation and use of psychoactive substances and support the design of interventions that address these risk factors to reduce and prevent subsequent harms.