bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection and analysis of long noncoding RNA expression profiles related to epithelial–mesenchymal transition in keloids
Authors: Chen Zhixiong , Chu Xi , Xu Jinghong 
Published: January 2022

Abstract
Background
The role of epithelial-mesenchymal transition (EMT) in the pathogenesis of keloids is currently raising increasing attention. Long noncoding RNAs (lncRNAs) govern a variety of biological processes, such as EMT, and their dysregulation is involved in many diseases including keloid disease. The aim of this study was to identify differentially expressed EMT-related lncRNAs in keloid tissues versus normal tissues and to interpret their functions.

Results
Eleven lncRNAs and 16 mRNAs associated with EMT were identified to have differential expression between keloid and normal skin tissues (fold change > 1.5, P < 0.05). Gene Ontology (GO) analysis showed that these differentially expressed mRNAs functioned in the extracellular matrix, protein binding, the positive regulation of cellular processes, the Set1C/COMPASS complex and histone acetyltransferase activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that these mRNAs are involved in pathways in cancer. The lncRNA, XLOC_000587 may promote cell proliferation and migration by enhancing the expression of ENAH, while AF268386 may facilitate the invasive growth of keloids by upregulating DDR2.

Conclusions
We characterized the differential expression profiles of EMT-related lncRNAs and mRNAs in keloids, which may contribute to preventing the occurrence and development of keloids by targeting the corresponding signaling pathways. These lncRNAs and mRNAs may provide biomarkers for keloid diagnosis and serve as potential targets for the treatment of this disease.
Significant co-expression of putative cancer stem cell markers, EpCAM and CD166, correlates with tumor stage and invasive behavior in colorectal cancer
Authors: Kalantari Elham , Taheri Tahereh , Fata Saba , Abolhasani Maryam , Mehrazma Mitra , Madjd Zahra , Asgari Mojgan 
Published: January 2022

AbstractBackgroundThe crucial oncogenic role of cancer stem cells (CSCs) in tumor maintenance, progression, drug resistance, and relapse has been clarified in different cancers, particularly in colorectal cancer (CRC). The current study was conducted to evaluate the co-expression pattern and clinical significance of epithelial cell adhesion molecules (EpCAM) and activated leukocyte cell adhesion (CD166 or ALCAM) in CRC patients.MethodsThis study was carried out on 458 paraffin-embedded CRC specimens by immunohistochemistry on tissue microarray (TMA) slides.ResultsElevated expression of EpCAM and CD166 was observed in 61.5% (246/427) and 40.5% (164/405) of CRC cases. Our analysis showed a significant positive association of EpCAM expression with tumor size (P= 0.02), tumor stage (P= 0.007), tumor differentiate (P= 0.005), vascular (P= 0.01), neural (P= 0.01), and lymph node (P= 0.001) invasion. There were no significant differences between CD166 expression and clinicopathological parameters. Moreover, the combined analysis demonstrated a reciprocal significant correlation between EpCAM and CD166 expression (P= 0.02). Interestingly, there was a significant positive correlation between EpCAM/CD166 phenotypes expression and tumor stage (P= 0.03), tumor differentiation (P= 0.05), neural, and lymph node invasion (P=0.01).ConclusionsThe significant correlation of EpCAM and CD166 expression and their association with tumor progression and aggressive behavior is the reason for the suggestion of these two CSC markers as promising targets to promote novel effective targeted-therapy strategies for cancer treatment in the present study.
Application of X-ray computed tomography to analyze the structure of sorghum grain
Authors: Crozier Daniel , Riera-Lizarazu Oscar , Rooney William L. 
Published: January 2022

Abstract
Background
The structural characteristics of whole sorghum kernels are known to affect end-use quality, but traditional evaluation of this structure is two-dimensional (i.e., cross section of a kernel). Current technology offers the potential to consider three-dimensional structural characteristics of grain. X-ray computed tomography (CT) presents one such opportunity to nondestructively extract quantitative data from grain caryopses which can then be related to end-use quality.

Results
Phenotypic measurements were extracted from CT scans of grain sorghum caryopses. Extensive phenotypic variation was found for embryo volume, endosperm hardness, endosperm texture, endosperm volume, pericarp volume, and kernel volume. CT derived estimates were strongly correlated with ground truth measurements enabling the identification of genotypes with superior structural characteristics.

Conclusions
Presented herein is a phenotyping pipeline developed to quantify three-dimensional structural characteristics from grain sorghum caryopses which increases the throughput efficiency of previously difficult to measure traits. Adaptation of this workflow to other small-seeded crops is possible providing new and unique opportunities for scientists to study grain in a nondestructive manner which will ultimately lead to improvements end-use quality.
Comparison between external locking plate fixation and conventional external fixation for extraarticular proximal tibial fractures: a finite element analysis
Authors: Blažević Dejan , Kodvanj Janoš , Adamović Petra , Vidović Dinko , Trobonjača Zlatko , Sabalić Srećko 
Published: January 2022

Abstract
Background
Good clinical outcomes for locking plates as an external fixator to treat tibial fractures have been reported. However, external locking plate fixation is still generally rarely performed. This study aimed to compare the stability of an external locking plate fixator with that of a conventional external fixator for extraarticular proximal tibial fractures using finite element analysis.

Methods
Three models were constructed: (1) external locking plate fixation of proximal tibial fracture with lateral proximal tibial locking plate and 5-mm screws (ELP), (2) conventional external fixation of proximal tibial fracture with an 11-mm rod and 5-mm Schanz screws (EF-11), and (3) conventional external fixation of a proximal tibial fracture with a 7-mm rod and 5-mm Schanz screws (EF-7). The stress distribution, displacement at the fracture gap, and stiffness of the three finite element models at 30-, 40-, 50-, and 60-mm plate–rod offsets from the lateral surface of the lateral condyle of the tibia were determined.

Results
The conventional external fixator showed higher stiffness than the external locking plate fixator. In all models, the stiffness decreased as the distance of the plate–rod from the bone surface increased. The maximum stiffness was 121.06 N/mm in the EF-11 model with 30-mm tibia–rod offset. In the EF-7 model group, the maximum stiffness was 40.00 N/mm in the model with 30-mm tibia–rod offset. In the ELP model group, the maximum stiffness was 35.79 N/mm in the model with 30-mm tibia–plate offset.

Conclusions
Finite element analysis indicated that external locking plate fixation is more flexible than conventional external fixation and can influence secondary bone healing. External locking plate fixation requires the placement of the plate as close as possible to the skin, which allows for a low-profile design because the increased distance from the plate to the bone can be too flexible for bone healing. Further experimental mechanical model tests are necessary to validate these finite element models, and further biological analysis is necessary to evaluate the effect of external locking plate fixation on fracture healing.
Protein intake and outcome of critically ill patients: analysis of a large international database using piece-wise exponential additive mixed models
Authors: Hartl Wolfgang H. , Kopper Philipp , Bender Andreas , Scheipl Fabian , Day Andrew G. , Elke Gunnar , Küchenhoff Helmut 
Published: January 2022

AbstractBackgroundProteins are an essential part of medical nutrition therapy in critically ill patients. Guidelines almost universally recommend a high protein intake without robust evidence supporting its use.MethodsUsing a large international database, we modelled associations between the hazard rate of in-hospital death and live hospital discharge (competing risks) and three categories of protein intake (low: < 0.8 g/kg per day, standard: 0.8–1.2 g/kg per day, high: > 1.2 g/kg per day) during the first 11 days after ICU admission (acute phase). Time-varying cause-specific hazard ratios (HR) were calculated from piece-wise exponential additive mixed models. We used the estimated model to compare five different hypothetical protein diets (an exclusively low protein diet, a standard protein diet administered early (day 1 to 4) or late (day 5 to 11) after ICU admission, and an early or late high protein diet).ResultsOf 21,100 critically ill patients in the database, 16,489 fulfilled inclusion criteria for the analysis. By day 60, 11,360 (68.9%) patients had been discharged from hospital, 4,192 patients (25.4%) had died in hospital, and 937 patients (5.7%) were still hospitalized. Median daily low protein intake was 0.49 g/kg [IQR 0.27–0.66], standard intake 0.99 g/kg [IQR 0.89– 1.09], and high intake 1.41 g/kg [IQR 1.29–1.60]. In comparison with an exclusively low protein diet, a late standard protein diet was associated with a lower hazard of in-hospital death: minimum 0.75 (95% CI 0.64, 0.87), and a higher hazard of live hospital discharge: maximum HR 1.98 (95% CI 1.72, 2.28). Results on hospital discharge, however, were qualitatively changed by a sensitivity analysis. There was no evidence that an early standard or a high protein intake during the acute phase was associated with a further improvement of outcome.ConclusionsProvision of a standard protein intake during the late acute phase may improve outcome compared to an exclusively low protein diet. In unselected critically ill patients, clinical outcome may not be improved by a high protein intake during the acute phase.Study registrationID numberISRCTN17829198
Epigenome-wide epidemiologic studies of human immunodeficiency virus infection, treatment, and disease progression
Authors: Titanji Boghuma K. , Gwinn Marta , Marconi Vincent C. , Sun Yan V. 
Published: January 2022

AbstractDespite significant advances in the treatment and care of people with HIV (PWH), several challenges remain in our understanding of disease pathogenesis to improve patient care. HIV infection can modify the host epigenome and as such can impact disease progression, as well as the molecular processes driving non-AIDS comorbidities in PWH. Epigenetic epidemiologic studies including epigenome-wide association studies (EWAS) offer a unique set of tools to expand our understanding of HIV disease and to identify novel strategies applicable to treatment and diagnosis in this patient population. In this review, we summarize the current state of knowledge from epigenetic epidemiologic studies of PWH, identify the main challenges of this approach, and highlight future directions for the field. Emerging epigenetic epidemiologic studies of PWH can expand our understanding of HIV infection and health outcomes, improve scientific validity through collaboration and replication, and increase the coverage of diverse populations affected by the global HIV pandemic. Through this review, we hope to highlight the potential of EWAS as a tool for HIV research and to engage more investigators to explore its application to important research questions.
Role of airway smooth muscle cell phenotypes in airway tone and obstruction in guinea pig asthma model
Authors: Álvarez-Santos Mayra D. , Álvarez-González Marisol , Eslava-De-Jesus Elizabeth , González-López Angel , Pacheco-Alba Ivonne , Pérez-Del-Valle Yazmín , Rojas-Madrid Rodrigo , Bazán-Perkins Blanca 
Published: January 2022

Abstract
Background
Airway obstruction (AO) in asthma is driven by airway smooth muscle (ASM) contraction. AO can be induced extrinsically by direct stimulation of ASM with contractile agonists as histamine, or by indirect provocation with antigens as ovalbumin, while the airway tone is dependent on intrinsic mechanisms. The association of the ASM phenotypes involved in different types of AO and airway tone in guinea pigs was evaluated.

Methods
Guinea pigs were sensitized to ovalbumin and challenged with antigen. In each challenge, the maximum OA response to ovalbumin was determined, and before the challenges, the tone of the airways. At third challenge, airway responsiveness (AR) to histamine was evaluated and ASM cells from trachea were disaggregated to determinate: (a) by flow cytometry, the percentage of cells that express transforming growth factor-β1 (TGF-β1), interleukin-13 (IL-13) and sarco-endoplasmic Ca2+ ATPase-2b (SERCA2b), (b) by RT-PCR, the SERCA2B gene expression, (c) by ELISA, reduced glutathione (GSH) and, (d) Ca2+ sarcoplasmic reticulum refilling rate by microfluorometry. Control guinea pig group received saline instead ovalbumin.

Results
Antigenic challenges in sensitized guinea pigs induced indirect AO, AR to histamine and increment in airway tone at third challenge. No relationship was observed between AO induced by antigen and AR to histamine with changes in airway tone. The extent of antigen-induced AO was associated with both, TGF-β1 expression in ASM and AR degree. The magnitude of AR and antigen-induced AO showed an inverse correlation with GSH levels in ASM. The airway tone showed an inverse association with SERCA2b expression.

Conclusions
Our data suggest that each type of AO and airway tone depends on different ASM phenotypes: direct and indirect AO seems to be sensitive to the level of oxidative stress; indirect obstruction induced by antigen appears to be influenced by the expression of TGF-β1 and the SERCA2b expression level plays a role in the airway tone.
Targeted gene suppression through double-stranded RNA application using easy-to-use methods in Arabidopsis thaliana
Authors: Park Minsu , Um Tae Young , Jang Geupil , Choi Yang Do , Shin Chanseok 
Published: January 2022

AbstractRNA interference (RNAi) is an RNA-dependent gene silencing process that is regulated by the interaction between the RNA-induced silencing complex (RISC) and double-stranded RNA (dsRNA). Exogenous dsRNAs are imported directly into the cytoplasm, where they are cleaved by Dicer into short dsRNA fragments of 20–25 base pairs. These short dsRNA fragments, called small interfering RNAs (siRNAs) have sequence-specific interaction with target genes. The guide strand, onto which siRNAs are incorporated in the RISC interacts with the target mRNA sequence, thereby inducing cleavage and degradation of target messenger RNAs (mRNAs) by ribonucleases. Recent studies have shown that plant dsRNA treatments can induce RNAi. However, the dsRNA application methods and delivery systems involved have not been well examined. In this study, dsRNA was introduced to Arabidopsis thaliana by two methods: dipping and spray. We synthesized two dsRNAs designed to target mRNAs encoding enhanced green fluorescent protein (EGFP). After applying dsRNAs that target EGFP, we found an obvious reduction in GFP expression. This was determined using fluorescence microscopy and quantitative reverse transcription PCR to assess the mRNA levels of the auxin-sensitive reporter DR5-EGFP Arabidopsis thaliana. Our data revealed that applying target gene-specific exogenous dsRNAs can induce suppression of target genes of interest whether the dipping or spray method is used. This study therefore provides a foundation for understanding how to apply and deliver dsRNAs in plants.
The materialization of the Buen Vivir and the Rights of Nature: Rhetoric and Realities of Guayaquil Ecológico urban regeneration project
Authors: Ordóñez María Fernanda , Shannon Kelly , d’Auria Viviana 
Published: January 2022

AbstractIn 2008, Ecuador became the first country in the world to declare nature as a subject of rights based on the ‘Buen Vivir’ (Good Living) philosophy which is premised on an indigenous principle that envisions a world where humans are part-and-parcel of a larger natural and social environment. Although Ecuador’s constitution is groundbreaking from a legal standpoint, the question arises of how the rights of nature is spatially manifested beyond the designation of protected areas? To shed light on such interrogation, this article, based on qualitative research, focuses on the linear park component of the mega-project Guayaquil Ecológico heralded as a first materialization which champions the “Rights of Nature” under the vision of the Buen Vivir. It unravels the contested rhetoric and realities of the Guayaquil Ecológico linear park in a critical review of the as-built project in relation to the larger objectives of Buen Vivir. The Guayaquil Ecologico linear park promised to simultaneously upgrade both social and environmental dimensions. However, it did not fully address the complexity of Guayaquil’s socio-ecological context and some of the structural injustices of the estuarine territory. Buen Vivir was rhetorically mobilised to implement a project where aesthetic dimensions dominated, further perpetuating socio-ecological vulnerabilities through relocation and evictions. Furthermore, its implementation was dependent on a specific political moment, leaving it in a state of abandonment and neglect. The Buen Vivir philosophy—as a decolonial stance that challenges western forms of development—can offer a fundamental base to question current modes of territorial occupation based on extractivist planning and design strategies. It holds significant potential to serve as base to re-think the relationship between forms of settlement, natural dynamics, and worldviews.
Response of potato (Solanum tuberosum L.) cultivars to drought stress under in vitro and field conditions
Authors: Zaki Haitham E. M. , Radwan Khlode S. A. 
Published: January 2022

Abstract
Background
Potato (Solanum tuberosum L.), the world’s third most important crop, is frequently thought to be sensitive to moderately sensitive to drought, and yield has fallen considerably over consecutive stress periods. Drought produces a wide range of responses in potato, from physiological alterations to variations in growth rates and yield. Knowledge about these responses is essential for getting a full understanding of drought-tolerance mechanism in potato plants which will help in the identification of drought-tolerant cultivars.

Results
A set of 21 commercial potato cultivars representing the genetic diversity in the Middle East countries market were screened for drought tolerance by measuring morpho-physiological traits and tuber production under in vitro and field trials. Cultivars were exposed to drought stress ranging from no drought to 0.1, 0.2 and 0.3 mol L−1 sorbitol in in vitro-based screening and 60, 40 and 20% soil moisture content in field-based screening. Drought stress adversely affected plant growth, yield and cultivars differed for their responses. Shoots and roots fresh weights, root length, surface area of root, no. of roots, no. of leaves, leaf area, plant water content %, K+ content, under in vitro drought treatments and shoots fresh and dry weights, no. of tubers and tuber yield under field drought treatments were examined and all decreased due to drought. The stress tolerance index decreased with increasing drought in examined cultivars; nevertheless, it revealed a degree of tolerance in some of them. Grouping cultivars by cluster analysis for response to drought resulted in: (i) a tolerant group of five cultivars, (ii) a moderately tolerant group of 11 cultivars, and (iii) a sensitive group of five cultivars. Furthermore, stress-related genes, i.e., DRO, ERECTA, ERF, DREB and StMYB were up-regulated in the five cultivars of the tolerant group. Likewise, the stomatal conductance and transpiration explained high correlation with the tuber yield in this group of cultivars.

Conclusion
The diversity in germplasm indicated that potato cultivars can be developed for production under certain degrees of drought. Some cultivars are good candidates to be included in drought-tolerant breeding programs and recommended for cultivation in drought-stricken regions.

Graphical Abstract
Application of melatonin-mediated modulation of drought tolerance by regulating photosynthetic efficiency, chloroplast ultrastructure, and endogenous hormones in maize
Authors: Ahmad Shakeel , Wang Guo Yun , Muhammad Ihsan , Farooq Saqib , Kamran Muhammad , Ahmad Irshad , Zeeshan Muhammad , Javed Tehseen , Ullah Saif , Huang Jing Hua , Zhou Xun Bo 
Published: January 2022

Abstract
Background
Melatonin played an essential role in numerous vital life processes of animals and captured the interests of plant biologists because of its potent role in plants as well. As far as its possible contribution to photoperiodic processes, melatonin is believed to act as a growth regulator and a direct free radical scavenger/indirect antioxidant. The objective of this study to identify a precise melatonin concentration for a particular application method to improve plant growth requires identification and clarification.

Methods
This work establishes unique findings by optimizing melatonin concentration in alleviating the detrimental effects of drought stress in maize. Maize plants were subjected to drought stress (40–45% FC) after treatments of melatonin soil drenching at different concentrations (50, 100, and 150 µM) to consider the changes of growth attribute, chlorophyll contents, photosynthetic rate, relative water content (RWC), chloroplast ultrastructure, endogenous hormonal mechanism, and grain yield.

Results
Our results showed that the application of melatonin treatments remarkably improved the plant growth attributes, chlorophyll contents, photosynthetic rate, RWC, hormonal mechanism, and grain yield plant−1 under drought conditions at a variable rate.

Conclusion
Our current findings hereby confirmed the mitigating potential of melatonin application 100 µM for drought stress by maintaining plant growth, hormone content, and grain yield of maize. We conclude that the application of melatonin to maize is effective in reducing drought stress tolerance.

Graphical Abstract
Teaching through urban sensorium: urban spatiality as a smart learning environment
Authors: Jayagopalan Gaana , Mukherjee Sweta 
Published: January 2022

AbstractThis paper qualitatively analyses the implication of urban sensorium as a pedagogic mode in the teaching of Urban Studies. Underpinned by the frames of smart learning environments, the paper reiterates experiencing urban ontologies as spatial learning environments. By drawing from a range of transdisciplinary and experiential modes of learning, this paper maps how an undergraduate course on Bangalore city in India served learners to critically engage with and experience spatial urban ontologies both digitally, and in real-world experiences of learning, furthering learner autonomy and reflection. The methodological prisms of this paper are autoethnography and critical reflection. It is organised around enabling learners recognize the experiential, embodied urban spaces through the urban sensorium via real-life engagements with urban spaces, and creation of digital portfolios that map this learning. Findings from the learners’ knowledge of sensory learning, the city’s intersectional aspects, and the student’s embodied and emplaced self in built environments and digital spaces are analysed via cognitive and affective-reflection levels; the course instructor's reflection is analysed via a process-reflection level. These reflections hold implications for the pedagogy of urban studies in undergraduate classrooms by foregrounding spatiality and urban sensorium as significant critical and affective pedagogic tools. The paper has also accommodated critical engagement with an external faculty member as a co-author, in order to manage any bias or researcher subjectivity in the design.