bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA:RNA hybrids at telomeres – when it is better to be out of the (R) loop
Authors: Toubiana Shir , Selig Sara 
Published: April 2018

R‐loops (RLs) are three‐stranded nucleic acid structures that contain a DNA:RNA hybrid and a displaced DNA strand. Genomic regions with GC skew and a G‐rich transcript are particularly prone to form RLs. RLs play important physiological roles in cells; however, when present at abnormally high levels, they may threaten genome stability. The perfect GC skew of telomeric repeats and the discovery of telomeric repeat‐containing RNA (TERRA), a long noncoding transcript that consists of the G‐rich telomeric sequence, make telomeric sequences the perfect candidates for generating RLs. Indeed, in the past 5 years, telomere R‐loops (TRLs) have been demonstrated in Saccharomyces cerevisiae, Trypanosoma brucei, and human cells. The presence of TRLs in normal human cells that transcribe low levels of TERRA, suggests a physiological role for these nucleic structures in telomere maintenance. Abnormally enhanced TERRA transcription, as found in several human pathological conditions, leads to high TRL levels and various cellular outcomes, depending on the recombinogenic capabilities of the cells. Study of TRLs in various organisms highlights the necessity for tight regulation of these structures, which can switch from beneficial to detrimental under different conditions. Here, we review the current state of knowledge on TRLs, describe several means by which TRLs are regulated, and discuss how findings from yeast are relevant to human pathological scenarios in which TRLs are deregulated.
Light‐weight thermal insulating fly ash cenosphere ceramics
Authors: Urunkar Yogesh , Pandit Aniruddha , Bhargava Parag , Joshi Jyeshtharaj , Mathpati Channamallikarjun , Vasanthakumaran Sudarsan , Jain Dheeraj , Hussain Zakir , Patel Shirish , More Venumadhav 
Published: April 2018

AbstractLight weight fly ash cenosphere (FAC) ceramic composites were developed by simple slip casting method. Thermal properties, Bulk density, Microstructure, flexural strength, and phase analysis of the FAC ceramic composites were measured. The results proved that the FAC have ability to lower bulk density and thermal conductivity effectively. The lowest thermal conductivity achieved for FAC ceramic composites (0.27 W/m.K) was further reduced 0.21 W/m.K by adding combustible additives ie activated charcoal and corn starch. The flexural strength, bulk density and thermal conductivity of FAC ceramic composites reduced consistently with an increase in FAC content. The maximum flexural strength of 13.45 MPa was achieved with 50% FAC and the minimum flexural strength of 4.07 MPa was obtained with 80% FAC. The open porosity increased from 35.51% to 43.76% and 38.19% with an addition of 15% activated charcoal and corn starch, respectively, when compared to no additives. The bulk density of 699, 619, and 675 kg/m3 was achieved with 80% FAC, 80% FAC with the addition of 15% activated charcoal and corn starch, respectively. The 80% FAC ceramic composite shows low thermal expansion coefficient 6.54 × 10−6/°C at the temperature of 50°C then it varies between 3.7 and 5 × 10−6/°C in the temperature range above 100°C. These results prove that the developed light weight FAC ceramic are excellent low‐cost thermal insulating materials.
Creep and relaxation of cement paste caused by stress‐induced dissolution of hydrated solid components
Authors: Li Xiaodan , Grasley Zachary C. , Bullard Jeffrey W. , Feng Pan 
Published: April 2018

AbstractThe creep and relaxation of cement paste caused by dissolving solid hydration products is evaluated in this work. According to the second law of thermodynamics, dissolution or precipitation of solid constituents may be altered by the change in stress/strain fields inside cement paste via alteration of the stress power or strain energy. Thus, it is hypothesized that stress‐induced dissolution can affect the overall creep/relaxation behavior of cement composites. A novel, fully coupled thermodynamic, mechanical, and microstructural model (TM2) that uses the finite element method was developed to predict the time‐evolving properties of cement paste under prescribed strains and to test the hypothesis. In the model, the strain energy was incorporated to accurately predict the effect of stress and strain fields on cement microstructure change. From the simulation results, depending on the stress/strain levels and the choice of the domain (over which the thermodynamic equilibrium is enforced), stress‐induced dissolution of solid constituents can lead to significant creep/relaxation.
A consensus statement on how to conduct inclusive health research
Authors: Frankena T. K. , Naaldenberg J. , Cardol M. , Garcia Iriarte E. , Buchner T. , Brooker K. , Embregts P. , Joosa E. , Crowther F. , Fudge Schormans A. , Schippers A. , Walmsley J. , O'Brien P. , Linehan C. , Northway R. , van Schrojenstein Lantman‐de Valk H. , Leusink G. 
Published: April 2018

AbstractBackgroundThe active involvement of people with intellectual disabilities in research, or inclusive research, is relatively common. However, inclusive health research is less common, even though it is expected to lead to appropriate healthcare and increased quality of life. Inclusive health research can build upon lessons learned from inclusive research.MethodA total of 17 experts on inclusive (health) research without intellectual disabilities and 40 experts with intellectual disabilities collaborated in this consensus statement. The consensus statement was developed in three consecutive rounds: (1) an initial feedback round; (2) a roundtable discussion at the 2016 International Association for the Scientific Study of Intellectual and Developmental Disabilities World Congress; and (3) a final feedback round.ResultsThis consensus statement provides researchers with guidelines, agreed upon by experts in the field, regarding attributes, potential outcomes, reporting and publishing, and future research directions, for designing and conducting inclusive health research.ConclusionsConsensus was reached on how to design and conduct inclusive health research. However, this statement should be continuously adapted to incorporate recent knowledge. The focus of this consensus statement is largely on inclusive health research, but the principles can also be applied to other areas.
Oleic acid enhances keratinocytes differentiation via the upregulation of miR‐203 in human epidermal keratinocytes
Authors: Kim Yun Jung , Lee Seong‐Beom , Lee Hyang Burm 
Published: April 2018

SummaryBackgroundOleic acid (OA) is an unsaturated free fatty acid (FFA) constituent of sebum. FFAs modulate keratinocyte differentiation. In this study, we determined whether OA affects keratinocyte differentiation in neonatal human epidermal keratinocytes (HEKn).MethodsHEKn was grown in EpiLife medium. The cells were treated with various concentrations of OA. The expression levels of keratin 10 and involucrin were determined using Western blotting (for the proteins) and quantitative real time polymerase chain reaction (qRT‐PCR) (for the mRNAs). Cytoskeletal changes were investigated by immunofluorescent staining. The levels of microRNA (miR)‐203 were determined by stem‐loop qRT‐PCR. The effect of miR‐203 on keratinocyte differentiation was evaluated using anti‐miR‐203.ResultsTreatment with OA promoted the expression of keratin 10 and involucrin, which are markers of spinous and granular layer keratinocytes, respectively. Treatment with OA also induced cell stratification and cytoskeletal changes such as the concentric ring organization of actin, a loss of planar polarity, and increased localization of epithelial cadherin (E‐cadherin) at cell‐cell contacts. OA increased the expression of miR‐203, which is associated with keratinocyte differentiation, and reduced the expression of p63, a target of miR‐203, in HEKn. Furthermore, transfection with anti‐miR‐203 suppressed the OA‐induced expression of involucrin.ConclusionsOleic acid accelerates keratinocyte differentiation via the upregulation of miR‐203 in HEKn under sub‐confluent conditions.
Effects of lactic acid bacteria and smectite after aflatoxin B1 challenge on the growth performance, nutrient digestibility and blood parameters of broilers
Authors: Liu N. , Ding K. , Wang J. , Deng Q. , Gu K. , Wang J. 
Published: April 2018

SummaryThis study aimed to investigate the effect of lactic acid bacteria (LAB) and smectite on the growth performance, nutrient digestibility and blood parameters of broilers that were fed diets contaminated with aflatoxin B1 (AFB1). A total of 480 newly hatched male Arbor Acres broilers were randomly allocated into four groups with six replicates of 20 chicks each. The broilers were fed diets with the AFB1 (40 μg/kg) challenge or without (control) it and supplemented with smectite (3.0 g/kg) or LAB (4.0 × 1010 CFU/kg) based on the AFB1 diet. The trial lasted for 42 days. The results showed that during days 1–42 of AFB1 challenge, the feed intake (FI) and body weight gain (BWG) were depressed (p < .05). The inclusion of LAB and smectite increased (p < .05) the BWG by 71.58 and 41.89 g/bird, respectively, which reached the level of the control diet (p ≥ .05), but there were no differences (p ≥ .05) in performance between LAB and smectite. LAB and smectite also increased (p < .05) the apparent total tract digestibility of the crude protein. Regarding the blood parameters, AFB1 decreased (p < .05) the levels of red blood cell count, haematocrit, mean corpuscular volume, haemoglobin, albumin and total protein. In the meantime, the AFB1 increased (p < .05) leucocyte counts, urea nitrogen, cholesterol, total bilirubin, creatinine, glutamic‐pyruvic transaminase, glutamic oxaloacetic transaminase and alkaline phosphatase. By contrast, LAB and smectite affected (p < .05) these parameters in the opposite direction. It can be concluded that after the AFB1 challenge, LAB and smectite have similar effects on the growth and health of the broilers, suggesting that LAB could be an alternative against AFB1 in commercial animal feeds.
Meaning, lived experience, empathy and boredom: Max van Manen on phenomenology and Heidegger
Authors: Paley John 
Published: April 2018

AbstractPhenomenology as Qualitative Research: A Critical Analysis of Meaning Attribution has attracted the attention of Max van Manen, who has published a highly critical review article. Anyone reading this article, but unfamiliar with the book, will get a distorted view of what it is about, whom it is addressed to, what it tries to achieve, and how it goes about presenting its arguments. Not mildly distorted, in need of the odd correction here and there, but systematically misrepresented. One problem is that van Manen appears to have an idée fixe which prevents him from recognizing that the book is not about a certain philosophical tradition (known as “phenomenology”), but about a particular type of qualitative research (also known, unfortunately and confusingly, as “phenomenology”). A second idée fixe disposes him to misread an earlier article of mine and (much more seriously) three works by Heidegger. My aim in this article is to describe these two idées fixes, and exhibit their consequences. In doing so, I will examine what van Manen has to say on four crucial topics: meaning, lived experience, empathy, and Heidegger's analysis of boredom in The Fundamental Concepts of Metaphysics.
Psychosocial predictors of medication non‐adherence in pediatric organ transplantation: A systematic review
Authors: Killian Michael O. , Schuman Donna L. , Mayersohn Gillian S. , Triplett Kelli N. 
Published: April 2018

AbstractAdherence to immunosuppressant medication is critical to health and quality‐of‐life outcomes for children who have received a solid organ transplant. Research on the psychological and social predictors of medication adherence is essential to the advancement of pretransplant assessments and transplant psychosocial services. Despite the importance of identifying risk factors, the literature remains limited regarding psychosocial predictors of non‐adherence. A systematic search was conducted to identify studies of the psychosocial predictors of post‐transplant medication non‐adherence in pediatric solid organ transplantation. From 1363 studies identified in searches of empirical literature, a final sample consisted of 54 publications representing 49 unique studies. Findings regarding psychosocial predictors were inconsistent with non‐adherence associated largely with adolescence, racial/ethnic minority status, and presence of mental health issues. Familial predictors of non‐adherence problems included single‐parent households, lower socioeconomic status, lower family cohesion, presence of family conflict, and poor family communication. Several studies reported an association between non‐adherence and social pressures (eg, peer social interaction, wanting to feel normal) among adolescent transplant recipients. While significant methodological and substantive gaps remain in this body of knowledge, this review synthesizes current evidence for assessment for transplant clinicians and researchers.
Molecular cloning and expression of FGF2 gene in pre‐implantation developmental stages of in vitro‐produced sheep embryos
Authors: Mor A , Mondal S , Reddy IJ , Nandi S , Gupta PSP 
Published: April 2018

ContentsEarly embryonic mortality is one of the main sources of reproductive loss in domestic ruminants including sheep. Fibroblast growth factor‐2 (FGF‐2) is a member of FGFs family that mediates trophoblast activities and regulates embryonic development in various species. In this study, we have cloned, characterized sheep FGF2 cDNA (KU316368) and studied the expression in sheep embryos. Ovaries of non‐pregnant sheep were collected from local abattoir and matured in culture medium at 38.5ºC, 5% CO2, 95% humidity for 22–24 hr. The matured oocytes were inseminated with capacitated spermatozoa in Brackett and Oliphant medium and resulted embryos were cultured in CO2 incubator for 6–7 days to complete the developmental stages from two cells to blastocyst stage. Total RNA was extracted from immature oocytes (n = 100), mature oocytes (n = 100) and different stages of embryos such as 2 cell (n = 50), 4 cell (n = 25), 8 cell (n = 12), 16 cell (n = 6), morula (n = 5) and blastocyst (n = 3). The total RNA isolated from the oocytes and embryos was reverse transcribed and subjected to real‐time polymerase chain reaction using sequence‐specific primers and SYBR green as the DNA dye. On sequence analysis, the nucleotide sequence of sheep FGF2 exhibited highest sequence similarity with cattle (100%) and least with rat and mouse (69.2%). At the deduced amino acid level, a highest degree of similarity was noticed with cattle, buffalo, goat, pig, camel and horse (100%) and lowest degree of identity with rat, human and mouse (98.2%). The FGF2 mRNA expression was higher in immature and mature oocytes and gradually decreases from 2‐cell stage of embryo to the blastocyst stage. More over a significant differences in FGF2 mRNA expression (p < .05) were observed between immature oocytes and all pre‐implantation stages of embryo. It can be concluded that FGF‐2 plays a significant role in pre‐implantation and early development of embryos in sheep.
Impact of limb weakness on extubation failure after planned extubation in medical patients
Authors: Jeong Byeong‐Ho , Nam Jimyoung , Ko Myeong Gyun , Chung Chi Ryang , Suh Gee Young , Jeon Kyeongman 
Published: April 2018

ABSTRACTBackground and objectiveLimb muscle weakness is associated with difficult weaning. However, there are limited data on extubation failure. The objective of this cohort study was to evaluate the association between limb muscle weakness according to the Medical Research Council (MRC) scale and extubation failure rates among patients in a medical intensive care unit (ICU).MethodsAll consecutive medical ICU patients who were mechanically ventilated for more than 24 h and who were weaned according to protocol were prospectively registered, and limb muscle weakness was assessed using the MRC scale on the day of planned extubation. Association of limb muscle weakness with extubation failure within 48 h following planned extubation was evaluated with logistic regression analysis.ResultsOver the study period, 377 consecutive patients underwent planned extubation through a standardized weaning process. Extubation failure occurred in 106 (28.1%) patients. Median scores on the MRC scale for four limbs were lower in patients with extubation failure (14, interquartile range (IQR) 12–16) than in patients without extubation failure (16, IQR 12–18; P = 0.024). In addition, extubation failure rates decreased significantly with increasing quartiles of MRC scores (P for trend <0.001). In multivariable analysis, MRC scores ≤10 points were independently associated with extubation failure within 48 h (adjusted OR 2.131, 95% CI: 1.071–4.240, P = 0.031).ConclusionLimb muscle weakness assessed on the day of extubation was found to be independently associated with higher extubation failure rates within 48 h following planned extubation in medical patients.
Some mitochondrial genes perform better for damselfly phylogenetics: species‐ and population‐level analyses of four complete mitogenomes of Euphaea sibling species
Authors: Cheng Yun‐Chieh , Chen Ming‐Yu , Wang Jo‐Fan , Liang Ai‐Ping , Lin Chung‐Ping 
Published: April 2018

AbstractAnimal mitochondrial genes continue to provide an efficient and inexpensive assessment of genetic diversity. However, which mitochondrial genes should be selected to best estimate species phylogeny and population genealogy remains uncertain for most under‐sampled taxa. We analysed four complete mitochondrial genomes of sibling species of Euphaea damselflies, E. decorata, E. ornata, E. formosa and E. yayeyamana (Insecta, Odonata, Euphaeidae), to examine the patterns of selection and to evaluate the phylogenetic utility of the mitochondrial genes compared with nuclear genes. The results indicated that mitochondrial protein‐coding nad2 (NADH dehydrogenase subunit 2) and noncoding A + T‐rich (control region) genes have the highest mutation rates and more phylogenetic utility [higher parsimony‐informative sites; higher α (the shape parameter of gamma distribution); lower rates of heterogeneity among sites; and higher relative substitution rates] than all the other mitochondrial and nuclear genes analysed. In contrast, the animal DNA barcoding gene cytochrome c oxidase subunit 1 (cox1) had average values for all estimated parameters of phylogenetic performance and was sometimes outperformed by other mitochondrial genes. The majority of the mitochondrial and nuclear genes in Euphaea damselflies have experienced frequent purifying selection, except for two cases of potential positive selection in NADH dehydrogenase subunit 3 (nad3) and elongation factor 1α (EF1α), and all mitochondrial genes had experienced stronger purifying selection than nuclear genes. Our findings indicated that mitochondrial nad2 and the A + T‐rich region should be selected to provide efficient and high‐resolution phylogenetic markers for damselflies at the species and population level.
Source of the Fitness Defect in Rifamycin-Resistant Mycobacterium tuberculosis RNA Polymerase and the Mechanism of Compensation by Mutations in the β′ Subunit
Authors: Stefan Maxwell A. , Ugur Fatima S. , Garcia George A. 
Published: April 2018

ABSTRACT

Mycobacterium tuberculosis
is a critical threat to human health due to the increased prevalence of rifampin resistance (RMP
r
). Fitness defects have been observed in RMP
r
mutants with amino acid substitutions in the β subunit of RNA polymerase (RNAP). In clinical isolates, this fitness defect can be ameliorated by the presence of secondary mutations in the double-psi β-barrel (DPBB) domain of the β′ subunit of RNAP. To identify factors contributing to the fitness defects observed
in vivo
, several
in vitro
RNA transcription assays were utilized to probe initiation, elongation, termination, and 3′-RNA hydrolysis with the wild-type and RMP
r
M. tuberculosis
RNAPs. We found that the less prevalent RMP
r
mutants exhibit significantly poorer termination efficiencies relative to the wild type, an important factor for proper gene expression. We also found that several mechanistic aspects of transcription of the RMP
r
mutant RNAPs are impacted relative to the wild type. For the clinically most prevalent mutant, the βS450L mutant, these defects are mitigated by the presence of secondary/compensatory mutations in the DPBB domain of the β′ subunit.
Complete Coding Sequences of Dengue Virus Type 2 Strains from Febrile Patients Seen in Malindi District Hospital, Kenya, during the 2017 Dengue Fever Outbreak
Authors: Gathii Kimita , Nyataya Josphat N. , Mutai Beth K. , Awinda George , Waitumbi John N. 
Published: April 2018

ABSTRACT
We report here 10 complete polyprotein-coding sequences of dengue virus type 2 strains isolated from febrile patients who presented at Malindi District Hospital, Kenya, during a recent dengue fever outbreak. Phylogenetically, all the strains belonged to clonal serotype 2 of the Cosmopolitan genotype.
Draft Genome Sequences of Three Ochrobactrum spp. Isolated from Different Avian Hosts in Pakistan
Authors: Sharma Poonam , Killmaster Lindsay F. , Volkening Jeremy D. , Cardenas-Garcia Stivalis , Wajid Abdul , Rehmani Shafqat Fatima , Basharat Asma , Miller Patti J. , Afonso Claudio L. 
Published: April 2018

ABSTRACT

Here, we present the draft genome sequences of three
Ochrobactrum
sp. strains with multidrug-resistant properties, isolated in 2015 from a pigeon and two chickens in Pakistan.
Draft Genome Sequences of Four Clinical Legionella pneumophila Isolates from Ontario, Canada
Authors: Fortuna Alexander , Ramnarine Ricardo , Li Aimin , Fittipaldi Nahuel , Frantz Christine , Mallo Gustavo V. 
Published: April 2018

ABSTRACT

Legionella pneumophila
outbreak investigations require the development of reliable typing methods to better understand the genetic relationships of the isolates involved. Here, we report the draft genome sequences of four clinical
Legionella pneumophila
isolates obtained between 2000 and 2012 in Ontario, Canada.