bluuebunny/crossref_metadata_2025_split huggingface dataset:
Base-pair Ambiguity and the Kinetics of RNA Folding
Authors: Zhou Guangyao , Loper Jackson , Geman Stuart 
Published: November 2019

Abstract
Background : A folding RNA molecule encounters multiple opportunities to form non-native yet energetically favorable pairings of nucleotide sequences. Given this forbidding free-energy landscape, mechanisms have evolved that contribute to a directed and efficient folding process, including catalytic proteins and error-detecting chaperones. Among structural RNA molecules we make a distinction between "bound" molecules, which are active as part of ribonucleoprotein (RNP) complexes, and "unbound," with physiological functions performed without necessarily being bound in RNP complexes. We hypothesized that unbound molecules, lacking the partnering structure of a protein, would be more vulnerable than bound molecules to kinetic traps that compete with native stem structures. We defined an "ambiguity index"---a normalized function of the primary and secondary structure of an individual molecule that measures the number of kinetic traps available to nucleotide sequences that are paired in the native structure, presuming that unbound molecules would have lower indexes. The ambiguity index depends on the purported secondary structure, and was computed under both the comparative ("gold standard") and an equilibrium-based prediction which approximates the minimum free energy (MFE) structure. Arguing that kinetically accessible metastable structures might be more biologically relevant than thermodynamic equilibrium structures, we also hypothesized that MFE-derived ambiguities would be less effective in separating bound and unbound molecules. Results : We have introduced an intuitive and easily computed function of primary and secondary structures that measures the availability of complementary sequences that could disrupt the formation of native stems on a given molecule---an ambiguity index. Using comparative secondary structures, the ambiguity index is systematically smaller among unbound than bound molecules, as expected. Furthermore, the effect is lost when the presumably more accurate comparative structure is replaced instead by the MFE structure. Conclusions : A statistical analysis of the relationship between the primary and secondary structures of non-coding RNA molecules suggests that stem-disrupting kinetic traps are substantially less prevalent in molecules not participating in RNP complexes. In that this distinction is apparent under the comparative but not the MFE secondary structure, the results highlight a possible deficiency in structure predictions when based upon assumptions of thermodynamic equilibrium.
Tacrolimus reverses the pemphigus vulgaris serum-enhanced expression of desmoglein in HaCaT cells
Authors: xie zhimin , Pan Qiaolin , Shen Xucheng , Zhang Yi , Dai Xiangnong , Ye Xingdong 
Published: November 2019

Abstract
Pemphigus vulgaris (PV) is associated with autoantibodies against desmoglein (Dsg), including Dsg1 and Dsg3. However, the precise mechanism by which acantholysis occurs in response to PV-IgG and the effect of tacrolimus for PV remain unclear.Method To co-culture human HaCaT keratinocytes with DMEM medium containing 5% PV-sera to establish a cell model of pemphigus that can determine the effect of PV-sera and tacrolimus on Dsg mRNA transcription and protein expression in HaCaT cells. Dsg protein expression in HaCaT cells was evaluated by Western blotting and Dsg mRNA transcription by real-time PCR (RT-PCR). The distribution of Dsg1 and Dsg3 in HaCaT cells was determined by indirect immunofluorescence (IIF).Results The application of 5% PV serum resulted in an increase in the transcription and expression levels of Dsg1 and Dsg3, whereas tacrolimus suppressed Dsg1 and Dsg3 expression. Tacrolimus inhibited PV serum-induced disruption of cell−cell contacts. Tacrolimus also downregulated the expression of Dsg1and Dsg3 compared with the PV group. IIF revealed that the linear deposits of Dsg1 on the surface of HaCaT cells in the PV-sera group disappeared and were replaced by granular and agglomerated fluorescent particles on the cell surface, whereas the Dsg3 linear deposits still existed, but this effect could be reversed by tacrolimus.Conclusion The Dsg3 antibody disrupts desmosome junctions by inducing endocytosis, resulting in desmosomal dissociation. Tacrolimus could reverse PV serum-induced enhancement Dsg expression in HaCaT cells.
The Barley Stripe Mosaic Virus expression system reveals the wheat C2H2 zinc finger protein TaZFP1B as a key regulator of drought tolerance
Authors: Houde Mario , Cheuk Arnaud , Ouellet François 
Published: November 2019

Abstract
Drought stress is one of the major factors limiting wheat production globally. Improving drought tolerance is important for agriculture sustainability. Although various morphological, physiological and biochemical responses associated with drought tolerance have been documented, the molecular mechanisms and regulatory genes that are needed to improve drought tolerance in crops require further investigation. We have used a novel 4-component version (for overexpression) and a 3-component version (for underexpression) of a barley stripe mosaic virus-based (BSMV) system for functional characterization of the C2H2-type zinc finger protein TaZFP1B in wheat. These expression systems avoid the need to produce transgenic plant lines and greatly speeds up functional gene characterization.Results We show that overexpression of TaZFP1B stimulates plant growth and up-regulates different oxidative stress-responsive genes under well-watered conditions. Plants that overexpress TaZFP1B are more drought tolerant at critical periods of the plant’s life cycle. Furthermore, RNA-Seq analysis revealed that plants overexpressing TaZFP1B reprogram their transcriptome, resulting in physiological and physical modifications that help wheat to grow and survive under drought stress. In contrast, plants transformed to underexpress TaZFP1B are significantly less tolerant to drought and growth is negatively affected.Conclusions This study clearly shows that the two versions of the BSMV system can be used for fast and efficient functional characterization of genes in crops. The extent of transcriptome reprogramming in plants that overexpress TaZFP1B indicates that the encoded transcription factor is a key regulator of drought tolerance in wheat.
XiangShaLiuJunZi Decoction combined with S-1 in the maintenance treatment of Stage III and IV Gastric Cancer: a protocol for a randomized controlled trial
Authors: Hong Xiao-Cui , Liang Qi-Lian , Luo Xing-Bo , Hu Ke-Hui , Yang Hai-Xia , Ou Wen-ting , Zhang Hui-Jie 
Published: November 2019

Abstract
Background The total effective rate of first-line chemotherapy based on fluorouracils and platinum for advanced gastric cancer is about 31%-64%, but most of Patients will develop worse after 3-8 months, while second-line chemotherapy is seems inefficient and prone to serious adverse chemotherapy reactions. The new oral fluorouracil chemotherapeutic drug, S-1, has been increasingly used in clinical maintenance after first-line chemotherapy for stage III and IV gastric cancer because of its its own advantages. In addition, the effects of XiangshaLiujunzi Decoction(XSLJZD) and other traditional Chinese medicines(TCM) on alleviating the side effects of chemotherapy and improving the quality of life of cancer patients have been gradually confirmed, no more reports about the maintenance treatment mode of combination of western medicine and TCM. We designed the trial of XSLJZD combined with S-1 in the maintenance treatment of Stage III and IV Gastric Cancer, hoped that this research program will go further and comprehensively evaluate its effectiveness, safety and superiority.Methods/design This trial is an open, Single-center, randomized trial. Patients with stage III and stage IV gastric cancer will be randomized into group A (S-1), group B (S-1 combined with XSLJZD), and group C (symptomatic treatment/observation) for five year of corresponding treatment. Accordingly, the primary endpoint of this trial was progression-free survival (PFS), along with the secondary end point was Overall survival(OS) and Quality of Life Assessment (QOLA), the latter includes improvement in symptoms before and after treatment, Karnofsky Performance Status (KPS), and adverse events (AEs) assessment.Discussion The results of this trial can uncover to some extent that S-1 or S-1 combined with XSLJZD on PFS, OS and QOLA in the maintenance period of stage III and IV gastric cancer, as well as provide a preliminary basis for the effectiveness of S-1 combined with XSLJZD in the maintenance period of stage III and IV gastric cancer.
A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes
Authors: Podell Sheila , Blanton Jessica M. , Oliver Aaron , Schorn Michelle A. , Agarwal Vinayak , Biggs Jason S. , Moore Bradley S. , Allen Eric E. 
Published: November 2019

Abstract
Background: Marine sponges and their microbiomes contribute significantly to carbon and nutrient cycling in global reefs, processing and remineralizing dissolved and particulate organic matter. Lamellodysidea herbacea sponges obtain additional energy from abundant photosynthetic Hormoscilla cyanobacterial symbionts, which also produce polybrominated diphenyl ethers (PBDEs) chemically similar to anthropogenic pollutants of environmental concern. Potential contributions of non-Hormoscilla bacteria to Lamellodysidea microbiome metabolism and the synthesis and degradation of additional secondary metabolites are currently unknown. Results: This study has determined relative abundance, taxonomic novelty, metabolic capacities, and secondary metabolite potential in 21 previously uncharacterized, uncultured Lamellodysidea-associated microbial populations by reconstructing near-complete metagenome-assembled genomes (MAGs) to complement 16S rRNA gene amplicon studies. Microbial community structures aligned with sponge host subgroup phylogeny in 16 samples from four host clades collected from multiple sites in Guam over a three year period, including representatives of Alphaproteobacteria, Gammaproteobacteria, Oligoflexia, and Bacteroidetes as well as Cyanobacteria (Hormoscilla). Unexpectedly, microbiomes from one host clade also included Cyanobacteria from the chemically talented genus Prochloron, a common tunicate symbiont. Two novel Alphaprotobacteria MAGs encoded pathways diagnostic for methylotrophic metabolism as well as Type III secretion systems, and have been provisionally assigned to a new order, designated Candidatus Methylospongiales. MAGs from other taxonomic groups encoded light-driven energy production pathways using not only chlorophyll, but also bacteriochlorophyll and proteorhodopsin. Diverse heterotrophic capabilities favoring aerobic versus anaerobic conditions included pathways for degrading chitin, eukaryotic extracellular matrix polymers, phosphonates, dimethylsulfoniopropionate, trimethylamine, and benzoate. Genetic evidence identified an aerobic catabolic pathway for halogenated aromatics that may enable endogenous PBDEs to be used as a carbon and energy source. Conclusions: The reconstruction of high quality MAGs from all microbial taxa comprising greater than 0.1% of the sponge microbiome enabled species-specific assignment of unique metabolic features that could not have been predicted from taxonomic data alone. This information will promote more representative models of marine invertebrate microbiome contributions to host bioenergetics, the identification of potential new sponge parasites and pathogens based on conserved metabolic and physiological markers, and a better understanding of biosynthetic and degradative pathways for secondary metabolites and halogenated compounds in sponge-associated microbiota.
The effect of combination of methanol with several concentration of honey solution on sperm quality of botia Chromobotia macracanthus Bleeker 1852 after short-term storage at −80 ℃
Authors: Abinawanto Abinawanto , Musthofa Siti Zuhriyyah , Lestari Retno , Bowolaksono Anom , Wilkes Martin , Muchlisin Zainal Abidin 
Published: November 2019

Abstract
Background: Clown loach or botia, Chromobotia macracanthus Bleeker 1852, is a popular freshwater ornamental fish. Lack of high quality broodstock and asynchronous gonad maturation are the main problem in breeding of this species. Cryopreservation is one of the methods to overcome this problem, and cryoprotectant plays a vital role in this process. Herein, we tested two types of cryoprotectants, namely methanol as a permeating cryoprotectant and honey solution as a natural non-permeating cryoprotectant. Hence, the objective of the present study was to determine best combination of honey solution and methanol for short-term storage of C. macracanthus sperm. Methods: One level of methanol (10%) combined with six levels of honey solution (0%, 0.1%, 0.3%, 0.5%, 0.7% and 0.9%) were tested in this study. Ringer’s solution was used as an extender. The diluted sperms were equilibrated for 25 min at 4 °C and then kept at −80 ℃ for 48 h. Sperms was thawed for 13 s at 40 °C. Spermatozoa viability, motility, and fertilization rates were then observed. Results: The one-way ANOVA showed that combination of methanol with several concentrations of honey had a significant effect on sperm viability and fertilization rates (P<0.05), but did have a significant effect on sperm motility (P>0.05). The study revealed that the 0.1% honey solution combined with 10% methanol resulted in the highest rates of motility (89.4 ± 5.45%), viability (85.75 ± 4.79 %), and fertilization (98.55 ± 1.69 %). Conclusion: A 0.1% honey solution combined with 10% methanol in Ringer’s was the best cryoprotectant for C. macracanthus spermatozoa preserved at -80 ℃.
Salmonella enterica serovar Typhimurium sseK3 induce cell apoptosis and enhance glycolysis in macrophages
Authors: Du Fuyu , Yu Chuan , Zhang Chunjie , Li Yinju , Liao Chengshui , He Lei , Cheng Xiangchao , Zhang Xiaojie 
Published: November 2019

Abstract
Background: Salmonella enterica serovar Typhimurium (S. Typhimurium) is an important infectious disease pathogen. Previous studies have identified that S. Typhimurium secreted effector K3 (SseK3) is a novel translated and secreted protein, but it is unclear whether this protein exerts a significant role in the progress of apoptosis and glycolysis in macrophages.
Results: The S. Typhimurium SL1344 wild-type (WT) group, ΔsseK3 mutant group and sseK3-complemented group were used to infect macrophages and the effects of sseK3 on apoptosis and glycolysis of macrophages were investigated. The adherence and invasion of ΔsseK3 mutant group for macrophages were similar to WT group and sseK3-complemented group, indicating that SseK3 did not play an important role in the adherence and invasion of S. Typhimurium for macrophages. However, the apoptosis percentage of the ΔsseK3 mutant group was much lower than WT group and sseK3-complemented group using flow cytometry. The caspase-3, caspase-8 and caspase-9 enzyme activity of the ΔsseK3 mutant group were decreased significantly compared with WT group and sseK3-complemented group, which suggested that sseK3 could improve the activities of caspase-3, caspase-8 and caspase-9 enzyme. We also found that the pyruvic acid level did not significantly change among ΔsseK3 mutant group, WT group and sseK3-complemented group, but the lactic acid level of ΔsseK3 mutant group was much lower than WT group and sseK3-complemented group. The ATP level of ΔsseK3 mutant group was remarkably higher than WT group and sseK3-complemented group. These indicated that the sseK3 enhanced the level of glycolysis of macrophages infected by S. Typhimurium.
Conclusions: Our data showed that the sseK3 of S. Typhimurium can promote macrophages apoptosis and influence glycolysis levels of macrophages. These results may give a better clue about the relationship between apoptosis and glycolysis in macrophages induced by S. Typhimurium sseK3.
Keywords: S. Typhimurium, sseK3, macrophages apoptosis, glycolysis
Neighborhood’s locality, walkability, and residents’ multimorbidity: Evidence from the China’s middle-aged and older population
Authors: Yu Xuexin , Zhang Wei 
Published: November 2019

Abstract
Background Neighborhood factors have gained increasing attention, while the role of neighborhood’s walkability and location have not been clarified in multimorbidity. In this study, we estimated the prevalence of 14 non-communicable chronic disease (NCDs) and depicted variations in the number of NCDs as a function of road type, urban-rural settings, neighborhood characteristics, and individual confounders. Methods Data came from China Health and Retirement Longitudinal Study 2011 National Baseline Survey. Negative binomial regression with clustered robust standard errors was employed to analyze variations in the number of NCDs among 13,414 Chinese middle-aged and older population. Results First, over 65% subjects had at least one NCDs, and over 35% had multiple NCDs. Arthritis (33.08%), hypertension (24.54%), and digestive disease (21.98%) were the most prevalent NCDs. There existed no urban-rural differences in multimorbidity after adjusted for neighborhood clustering variations. Lastly, living with paved road was associated with fewer NCDs relative to living with unpaved road. Conclusion Findings suggest that urban-rural disparities in the number of NCDs appeared to result from within-neighborhoods characteristics. Living with walkable road is important for middle-aged and older population.
Primary Ovarian Leiomyoma: A common tumor in rare location and report of eight cases
Authors: zaigui wu , minyue Dong 
Published: November 2019

Abstract
Background: Leiomyomas are the most common pelvic tumors in fertile women and rare conditions of them have extrauterine locations. Ovarian Leiomyoma accounts only for 0.5 to 1% of all benign ovarian tumors with fewer than 60 cases reported in a manner of case report. Here we present a series of eight patients over a six-year period(2012-2018). The clinico-pathological features, diagnosis and management were discussed.
Case presentation: We had experienced eight cases of ovarian leiomyoma.The clinical features,pathologic findings,diagnosis, treatment were reviewed. The mean age of these patients was 38.5 years. The majority of these patients may be asymptomatic and usually diagnosed incidentally during pelvic examination or pathologic examination after surgery. Six cases presented only with pelvic mass sized from 2 to 20 cm and even some patients persisted for more than twenty years while the other two were diagnosed due to four years of primary infertile or three months of irregular vagina bleeding. Three patients coincident with uterine leiomyoma while the others not. Three had ovarian leiomyoma degenerated and one case had a evidence of atypical 4/10.
Conclusions : ovarian leiomyoma was very rare but it should be considered in the diagnosis of pelvic or ovarian solid masses. Magnetic resonance imaging was provital in its different diagnose while fast frozen pathology during operation was very necessary for its surgical decision. A proper surgical decision should be made according to patients age.
A metabolic profiling analysis of degenerative intervertebral disc disease in a rabbit model via GC/TOF-MS
Authors: Wu Xiaolin , Xiang Hongfei , Zhang Guoqing , Hu Yougu , wang yan , Chen Bohua 
Published: November 2019

Abstract
Background: To establish an analytical method for studying intervertebral disc metabolomics based on gas chromatography/time-of-flight mass spectrometry (GC/TOF-MS). Methods: To establish a rabbit model of intervertebral disc degeneration, the intervertebral discs of six New Zealand white rabbits were punctured. GC/TOF-MS was applied to analyze degenerated discs of the six model group animals and six similar New Zealand white rabbits considered as the control group. Pattern recognition and nonparametric test analyses were utilized to evaluate the data as well as screen for and identify significant biomarkers. Metabolites and metabolic pathways relevant to associated pathological processes were studied. Results: We established a rabbit model of intervertebral disc degeneration and an orthogonal partial least squares-discriminant analysis (OPLS-DA) disease-distinguishing model of intervertebral disc degeneration for contrast against the typical physiological state of intervertebral discs. Expression of six metabolites in degenerated and normal intervertebral discs of New Zealand white rabbits was evaluated. Levels of four metabolites expressed in the model group were significantly higher than in the control group, while two other metabolites were expressed at significantly lower levels in the model group as compared to the control group. Conclusions: This paper demonstrates that metabolic profiling of both degenerated and normal intervertebral rabbit discs is a feasible method of metabolomic analysis. Via in-depth filtering of characteristic metabolites, we found a high correlation between metabolic variations and intervertebral disc degeneration. Further studies on endogenous metabolites and pathways involved in intervertebral disc degeneration will provide a better understanding of associated molecular mechanisms and lay foundations for effective clinical treatment.
La escuela teledirigida o educación 2.0. una reflexión en contra del rebaño digital
Authors: Campiño Rojas Carlos Geovanny 
Published: November 2019

“La escuela teledirigida o educación 2.0. Una reflexión en contra del rebaño digital” es el resultado de una investigación minuciosa centrada alrededor de la órbita del fenómeno posmoderno y su aliado estratégico, conocido con el nombre de “era de la información”. En este orden de ideas, y amparados bajo el insumo de la pedagogía crítica, se pretenden evidenciar los objetos de seducción y demanda que maquinan al interior de la anatomía y arquitectura educativa postmoderna; parcialidad Colombia, empeñada actualmente en alienar, desmantelar y configurar la subjetividad de docentes y estudiantes desde influjos contraculturales cargados de hibridación cultural, imperio efímero de la moda, cultura digital y capitalismo cognitivo. En consecuencia, se espera armar un plan de contingencia capaz de contrarrestar los señuelos ideológicos que han penetrado con fuerza en la urdimbre educativa, a tal punto de inaugurar nuevas lógicas de poder, empotradas en la arista de la era de la información, quien amenaza con reducir sistemáticamente a los establecimientos educativos latinoamericanos a la mera consideración de pequeños relatos de naturaleza líquida y flotante, condenados a una potencial vía de extinción. Orientadas bajo la brújula de la metamorfosis educativa, se pretende, finalmente, dar respuesta al malestar digital presente, así como preparar a la comunidad educativa para contrarrestar su intensidad y transformar la realidad social de los contextos vulnerables a su accionar.
Palabras clave: Aldea global, postmodernidad, cultura digital, homo tecnologicus, globalización, pedagogía crítica, cibercultura, E-learning, capitalismo cognitivo.
Artes marciais na Educação Infantil: desafios e possibilidades
Authors: Pereira Araújo Leandro , Cerignoni Benites Larissa , Venâncio Ananias Elisângela , Preichardt Duek Viviane 
Published: November 2019

O relato descreve uma experiência de ensino com um grupo de crianças de cinco e seis anos, apontando desafios e possibilidades da inserção de Artes Marciais nas aulas de educação física infantil. As intervenções indicaram que a aprendizagem desse conteúdo foi motivante, contribuindo para desmistificar ideias relacionadas à violência e gênero. Concluímos que o ensino das lutas é possível, mediante adequações do espaço e materiais, de modo a respeitar as características da instituição e do público, especialmente as crianças.