bluuebunny/crossref_metadata_2025_split huggingface dataset:
Screening for mouse genes lost in mammals with long lifespans
Authors: Rubanov Lev I. , Zaraisky Andrey G. , Shilovsky Gregory A. , Seliverstov Alexandr V. , Zverkov Oleg A. , Lyubetsky Vassily A. 
Published: November 2019

Abstract

Background
Gerontogenes include those that modulate life expectancy in various species and may be the actual longevity genes. We believe that a long (relative to body weight) lifespan in individual rodent and primate species can be due, among other things, to the loss of particular genes that are present in short-lived species of the same orders. These genes can also explain the widely different rates of aging among diverse species as well as why similarly sized rodents or primates sometimes have anomalous life expectancies (e.g., naked mole-rats and humans). Here, we consider the gene loss in the context of the prediction of Williams’ theory that concerns the reallocation of physiological resources of an organism between active reproduction (r-strategy) and self-maintenance (K-strategy). We have identified such lost genes using an original computer-aided approach; the software considers the loss of a gene as disruptions in gene orthology, local gene synteny or both.

Results
A method and software identifying the genes that are absent from a predefined set of species but present in another predefined set of species are suggested. Examples of such pairs of sets include long-lived vs short-lived, homeothermic vs poikilothermic, amniotic vs anamniotic, aquatic vs terrestrial, and neotenic vs nonneotenic species, among others. Species are included in one of two sets according to the property of interest, such as longevity or homeothermy. The program is universal towards these pairs, i.e., towards the underlying property, although the sets should include species with quality genome assemblies. Here, the proposed method was applied to study the longevity of Euarchontoglires species. It largely predicted genes that are highly expressed in the testis, epididymis, uterus, mammary glands, and the vomeronasal and other reproduction-related organs. This agrees with Williams’ theory that hypothesizes a species transition from r-strategy to K-strategy. For instance, the method predicts the mouse gene Smpd5, which has an expression level 20 times greater in the testis than in organs unrelated to reproduction as experimentally demonstrated elsewhere. At the same time, its paralog Smpd3 is not predicted by the program and is widely expressed in many organs not specifically related to reproduction.

Conclusions
The method and program, which were applied here to screen for gene losses that can accompany increased lifespan, were also applied to study reduced regenerative capacity and development of the telencephalon, neoteny, etc. Some of these results have been carefully tested experimentally. Therefore, we assume that the method is widely applicable.
Effects of motor imagery training of Parkinson's disease: a protocol for a randomized clinical trial
Authors: Nascimento Isaíra Almeida Pereira da Silva , Santiago Lorenna Marques de Melo , de Souza Aline Alves , Pegado Camila de Lima , Ribeiro Tatiana Souza , Lindquist Ana Raquel Rodrigues 
Published: November 2019

Abstract

Background
Gait disorders in individuals with Parkinson’s disease (PD) may be associated with alterations in the motor control system and aggravated by psychoemotional and cognitive issues. Therapeutic strategies aimed at self-perception and motor regulation seem to be promising. Motor imagery (MI) has been shown to be one of these strategies, but there is still no clear evidence of its applicability in this population. The aim of this trial is to determine the effects of motor-imagery training on the gait and electroencephalographic activity of individuals with PD.

Methods/design
The sample will consist of 40 individuals, aged between 45 and 75 years, in the mild and moderate phase of the disease, with the ability to generate voluntary mental images. They will be assessed for cognitive level, degree of physical disability, mental-image clarity, kinematic gait variables, electroencephalographic activity and mobility. Next, subjects will be randomly assigned to an experimental group (EG) and a control group (CG). The EG will perform motor imagery and gait, while the CG will only engage in gait exercises. Twelve training sessions will be conducted lasting up to 90 min each, three times a week, for 4 weeks. The subjects will be reassessed on the kinematic variables of gait, electroencephalographic activity and mobility at 1, 7 and 30 days after the final training session.

Discussion
The results may provide an important advance in neurological rehabilitation where an easy-access and low-cost intervention may help to improve gait, electroencephalographic activity and mobility in individuals with PD.

Trial registration
Clinicaltrials.gov, ID: NCT03439800. Registered on 15 November 2017.
Designing and using incentives to support recruitment and retention in clinical trials: a scoping review and a checklist for design
Authors: Parkinson Beth , Meacock Rachel , Sutton Matt , Fichera Eleonora , Mills Nicola , Shorter Gillian W. , Treweek Shaun , Harman Nicola L , Brown Rebecca C. H. , Gillies Katie , Bower Peter 
Published: November 2019

Abstract

Background
Recruitment and retention of participants are both critical for the success of trials, yet both remain significant problems. The use of incentives to target participants and trial staff has been proposed as one solution. The effects of incentives are complex and depend upon how they are designed, but these complexities are often overlooked. In this paper, we used a scoping review to ‘map’ the literature, with two aims: to develop a checklist on the design and use of incentives to support recruitment and retention in trials; and to identify key research topics for the future.

Methods
The scoping review drew on the existing economic theory of incentives and a structured review of the literature on the use of incentives in three healthcare settings: trials, pay for performance, and health behaviour change. We identified the design issues that need to be considered when introducing an incentive scheme to improve recruitment and retention in trials. We then reviewed both the theoretical and empirical evidence relating to each of these design issues. We synthesised the findings into a checklist to guide the design of interventions using incentives.

Results
The issues to consider when designing an incentive system were summarised into an eight-question checklist. The checklist covers: the current incentives and barriers operating in the system; who the incentive should be directed towards; what the incentive should be linked to; the form of incentive; the incentive size; the structure of the incentive system; the timing and frequency of incentive payouts; and the potential unintended consequences. We concluded the section on each design aspect by highlighting the gaps in the current evidence base.

Conclusions
Our findings highlight how complex the design of incentive systems can be, and how crucial each design choice is to overall effectiveness. The most appropriate design choice will differ according to context, and we have aimed to provide context-specific advice. Whilst all design issues warrant further research, evidence is most needed on incentives directed at recruiters, optimal incentive size, and testing of different incentive structures, particularly exploring repeat arrangements with recruiters.
The model of local axon homeostasis - explaining the role and regulation of microtubule bundles in axon maintenance and pathology
Authors: Hahn Ines , Voelzmann André , Liew Yu-Ting , Costa-Gomes Beatriz , Prokop Andreas 
Published: November 2019

AbstractAxons are the slender, cable-like, up to meter-long projections of neurons that electrically wire our brains and bodies. In spite of their challenging morphology, they usually need to be maintained for an organism's lifetime. This makes them key lesion sites in pathological processes of ageing, injury and neurodegeneration. The morphology and physiology of axons crucially depends on the parallel bundles of microtubules (MTs), running all along to serve as their structural backbones and highways for life-sustaining cargo transport and organelle dynamics. Understanding how these bundles are formed and then maintained will provide important explanations for axon biology and pathology. Currently, much is known about MTs and the proteins that bind and regulate them, but very little about how these factors functionally integrate to regulate axon biology. As an attempt to bridge between molecular mechanisms and their cellular relevance, we explain here the model of local axon homeostasis, based on our own experiments in Drosophila and published data primarily from vertebrates/mammals as well as C. elegans. The model proposes that (1) the physical forces imposed by motor protein-driven transport and dynamics in the confined axonal space, are a life-sustaining necessity, but pose a strong bias for MT bundles to become disorganised. (2) To counterbalance this risk, MT-binding and -regulating proteins of different classes work together to maintain and protect MT bundles as necessary transport highways. Loss of balance between these two fundamental processes can explain the development of axonopathies, in particular those linking to MT-regulating proteins, motors and transport defects. With this perspective in mind, we hope that more researchers incorporate MTs into their work, thus enhancing our chances of deciphering the complex regulatory networks that underpin axon biology and pathology.
Benzimidazole Schiff base derivatives: synthesis, characterization and antimicrobial activity
Authors: Fonkui Thierry Youmbi , Ikhile Monisola Itohan , Njobeh Patrick Berka , Ndinteh Derek Tantoh 
Published: November 2019

Abstract
A series of Schiff bases (3.a–f) bearing benzimidazole moiety was successfully synthesized in ethanol by refluxing Oct-2-ynoic acid (1,3-dihydrobenzimidazole-2-ylidene)amide with substituted amines. Fourier transform infrared (FTIR), ultra violet light (UV–VIS), elemental analysis, proton (1H) and carbon (13C) nuclear magnetic resonance spectroscopy were used to characterize the newly synthesized Schiff bases. Micro dilution method was used to determine the minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) of the Schiff bases, against 14 human pathogenic bacteria (8 Gram negative and 6 Gram positive) and against 7 fungal strains (5 Aspergillus and 2 Fusarium) representatives. Antimalarial activity against Plasmodium falciparum and antitrypanosomal property against Trypanosoma brucei was studied in vitro at a single dose concentration of the Schiff bases. Cytotoxicity of the Schiff bases was assessed against human cervix adenocarcinoma (HeLa) cells. Results obtained show that the newly synthesized Schiff bases are very potent antimicrobial agents. Gram negative bacteria Klebsiella pneumonia and Escherichia coli were more affected on exposure to Compounds 3.c–f (MIC 7.8 µg/mL) which in turn exhibited more antibacterial potency than nalidixic acid reference drug that displayed MICs between 64 and 512 µg/mL against K. pneumonia and E. coli respectively. The test compounds also demonstrated high cytotoxic effect against Aspergillus flavus and Aspergillus carbonarius as they displayed MFC 7.8 and 15.6 µg/mL. Compound 3.c exhibited the highest fungicidal property from this series with MFC alternating between 7.8 and 15.6 µg/mL against the investigated strains. The malarial activity revealed Compounds 3.c and 3.d as the more potent antiplasmodial compounds in this group exhibiting 95% and 85% growth inhibition respectively. The IC50 of Compounds 3.c and 3.d were determined and found to be IC50 26.96 and 28.31 µg/mL respectively. Compound 3.a was the most cytotoxic agent against HeLa cells in this group with 48% cell growth inhibition. Compounds 3.c, 3.d and 3.f were biocompatible with HeLa cells and displayed low toxicity. With a very low cytotoxic effect against HeLa, compound 3.c stands out to be a very good antiparasitic agent and consideration to further evaluate the candidate drug against others cell lines is necessary.
Study of the mechanism of change in flavonoid composition in the processing of Chrysanthemum morifolium (Ramat.) Tzvel. ‘Boju’
Authors: Zhang Wei , Zuo Yafeng , Xu Fengqing , Wang Tongsheng , Liu Jinsong , Wu Deling 
Published: November 2019

Abstract
A form of β-glucosidase was isolated and purified from fresh Chrysanthemum morifolium (Ramat.) Tzvel. ‘Boju’ (Boju) and its enzymatic properties explored in this study. The purified enzyme and Boju flavonoids were reacted in a water bath to ascertain the composition of the reactants. Flavonoid glycoside and aglycon concentrations in Boju varied significantly depending on processing method. The concentration of flavonoid glycosides in Boju decreased and flavonoid aglycons increased due to heat-activation of β-glucosidase which hydrolyzed the flavonoid glycosides in Boju to aglycons.
A novel electrochemical aptasensor for fumonisin B1 determination using DNA and exonuclease-I as signal amplification strategy
Authors: Wei Min , Zhao Fei , Feng Shuo , Jin Huali 
Published: November 2019

Abstract
In this work, using DNA and exonuclease-I (Exo-I) as signal amplification strategy, a novel and facile electrochemical aptasensor was constructed for fumonisin B1 (FB1) detection. The G-rich complementary DNA (cDNA) was immobilized onto the electrode surface. Then, aptamer of FB1 was hybridized with cDNA to form double-stranded DNA. In the absence of FB1, double-stranded DNA and G-rich cDNA on the electrode surface promoted effectively methylene blue (MB) enrichment and amplified the initial electrochemical response. In the presence of FB1, the combination of aptamer and FB1 led to the release of aptamer from the electrode surface and the expose of 3′ end of single-stranded cDNA. When Exo-I was added onto the electrode surface, the single-stranded cDNA was degraded in the 3′–5′ direction. The decrease of double-stranded DNA and G-rich cDNA resulted in the less access of MB to the electrode surface, which decreased the electrochemical signal. The experimental conditions including incubation time of FB1, the amount of Exo-I and incubation time of Exo-I were optimized. Under the optimal conditions, the linear relationship between the change of peak current and the logarithmic concentration of FB1 was observed in the range of 1.0 × 10−3–1000 ng mL−1 with a low limit of detection of 0.15 pg mL−1. The experimental results showed that the prepared aptasensor had acceptable specificity, reproducibility, repeatability and stability. Therefore, this proposed aptasensor has a potential application in the food safety detection.
Effects of ghrelin supplementation on the acute phase of Chagas disease in rats
Authors: de Paula Silva Ferdinando , da Costa Cássia Mariana Bronzon , Pereira Luiz Miguel , Lessa Diego Fernando Silva , Pitol Dimitrius Leonardo , Issa João Paulo Mardegan , do Prado Júnior José Clóvis , Abrahão Ana Amélia Carraro 
Published: November 2019

AbstractBackgroundTrypanosoma cruziis the causative agent of Chagas disease, which is endemic to subtropical and tropical Americas. The disease treatment remains partially ineffective, involving therapies directed to the parasite as well as palliative strategies for the clinical manifestations. Therefore, novel candidates for disease control are necessary. Additionally, strategies based on parasite inhibitionviaspecific targets and application of compounds which improve the immune response against the disease is welcomed. Ghrelin is a peptide hormone pointed as a substance with important cardioprotective, vasodilatory, anti-apoptotic, anti-oxidative and immune modulatory functions. The aims of this study were to evaluate the immunomodulatory effects of ghrelin in male Wistar rats infected with the Y strain ofT. cruzi.MethodsIn order to delineate an immune response againstT. cruzimediated by ghrelin, we evaluated the following parameters: quantification of blood and cardiac parasites; analysis of cell markers (CD3+, CD8+, NK, NKT, CD45RA+, macrophage and RT1B+); nitric oxide (NO) production; lymphoproliferation assays; splenocyte apoptosis; and INF-γ, IL-12 and IL-6 quantification in sera.ResultsThe animals infected withT. cruziand supplemented with ghrelin demonstrated an upregulated pattern in macrophage and NO production, whereas an anti-inflammatory response was observed in T cells and cytokines. The low response againstT. cruzimediated by T cells probably contributed to a higher colonization of the cardiac tissue, when compared to infected groups. On the other side, the peptide decreased the inflammatory infiltration in cardiac tissue infected withT. cruzi.ConclusionsGhrelin demonstrated a dual function in animals infected withT. cruzi. Further studies, especially related to the decrease of cardiac tissue inflammation, are needed in order to determine the advantages of ghrelin supplementation in Chagas disease, mostly for populations from endemic areas.
The feasibility of developing biomarkers from peripheral blood mononuclear cell RNAseq data in children with juvenile idiopathic arthritis using machine learning approaches
Authors: Poppenberg Kerry E. , Jiang Kaiyu , Li Lu , Sun Yijun , Meng Hui , Wallace Carol A. , Hennon Teresa , Jarvis James N. 
Published: November 2019

Abstract

Background
The response to treatment for juvenile idiopathic arthritis (JIA) can be staged using clinical features. However, objective laboratory biomarkers of remission are still lacking. In this study, we used machine learning to predict JIA activity from transcriptomes from peripheral blood mononuclear cells (PBMCs). We included samples from children with Native American ancestry to determine whether the model maintained validity in an ethnically heterogeneous population.

Methods
Our dataset consisted of 50 samples, 23 from children in remission and 27 from children with an active disease on therapy. Nine of these samples were from children with mixed European/Native American ancestry. We used 4 different machine learning methods to create predictive models in 2 populations: the whole dataset and then the samples from children with exclusively European ancestry.

Results
In both populations, models were able to predict JIA status well, with training accuracies > 74% and testing accuracies > 78%. Performance was better in the whole dataset model. We note a high degree of overlap between genes identified in both populations. Using ingenuity pathway analysis, genes from the whole dataset associated with cell-to-cell signaling and interactions, cell morphology, organismal injury and abnormalities, and protein synthesis.

Conclusions
This study demonstrates it is feasible to use machine learning in conjunction with RNA sequencing of PBMCs to predict JIA stage. Thus, developing objective biomarkers from easy to obtain clinical samples remains an achievable goal.
Investigation of molecular mechanisms underlying tetracycline resistance in thermophilic Campylobacter spp. suggests that previous reports of tet(A)-mediated resistance in these bacteria are premature
Authors: Lynch Caoimhe , Hawkins Kayleigh , Lynch Helen , Egan John , Bolton Declan , Coffey Aidan , Lucey Brigid 
Published: November 2019

Abstract
The true prevalence of tet(A), which codes for a tetracycline efflux pump, in thermophilic Camplyobacter spp. requires clarification after reports emerged in Iran (2014) and Kenya (2016) of the novel detection of tet(A) in Campylobacter. During our investigation of antibiotic resistance mechanisms in a sample of Irish thermophilic Campylobacter broiler isolates, it was determined that 100% of tetracycline-resistant isolates (n = 119) harboured tet(O). Accessory tetracycline-resistance mechanisms were considered as tetracycline minimum inhibitory concentrations ranged from 4 to ≥ 64 mg/L. Primers previously reported for the detection of tet(A) in Campylobacter failed to produce an amplicon using a positive control strain (Escherichia coli K12 SK1592 containing the pBR322 plasmid) and a selection of Campylobacter isolates. Accordingly, we designed new tet(A)-targeting primers on SnapGene2.3.2 that successfully generated a 407 bp product from the positive control strain only. Further in silico analysis using BLASTn and SnapGene2.3.2 revealed that previously reported Campylobacter tet(A) sequences deposited on GenBank shared 100% homology with Campylobacter tet(O). We postulate that this gave rise to the erroneous report of a high tet(A) prevalence among a pool of Kenyan broiler Campylobacter isolates that were tested using primers designed based on these apparent tet(A) sequences. In conclusion, further work would be required to determine whether the homology between tet(A) potentially present in Campylobacter and known tet(A) genes would be sufficient to allow amplification using the primers designed in our study. Finally, the existence of tet(A) in thermophilic Campylobacter spp. remains to be demonstrated.
Intention to use long-acting and permanent contraceptive methods and associated factors in health institutions of Aksum Town, North Ethiopia
Authors: Syum Hailay , Kahsay Gizienesh , Huluf Teklehaymanot , Beyene Berhe , Gerensea Hadgu , Gidey Gebreamlak , Desta Haftom , Abay Mebrahtu , Nuguse Haben , Haile Kebede 
Published: November 2019

Abstract

Objective
In Ethiopia, the majority of married women practice predominantly short-acting contraceptive methods. Therefore this study aims to assess intention to use LAPMs and its determinants among short-acting users in Health Institutions of Aksum Town, North Ethiopia.

Results
Prevalence of intention to use LAPMs was 52.1% (95% CI 47.4–57.0). Good knowledge on LAPMs [AOR = 2.15; 95% CI (1.29, 3.56)], positive attitude towards LAPMs [AOR = 3.41; 95% CI (1.99, 5.85)], 18–24 years of age [AOR = 3.18; 95% CI (1.30, 7.79)], being primary school in educational level [AOR = 0.34; 95% CI (0.14, 0.78)], decision on the number of children jointly with partner [AOR = 2.05; 95% CI (1.01, 4.18)], having more than two children [AOR = 10.67; 95% CI (1.29, 88.31)], and no [AOR = 10.21; 95% CI (3.10, 33.58)] and one [AOR = 4.70; 95% CI (1.68, 13.13)] extra number of children desired were factors significantly associated with having intention to use LAPMs compared to their counterparts. The intention to use LAPMs was low. Therefore, appropriate information, education and communication strategies must be designed to raise awareness and change the negative attitude of the community on LAPMs.
Connecting two worlds: positive correlation between physicochemical approach with blood gases and pH in pediatric ICU setting
Authors: Chaiyakulsil Chanapai , Mueanpaopong Papope , Lertbunrian Rojjanee , Chutipongtanate Somchai 
Published: November 2019

Abstract

Objective
Physicochemical approach such as strong ion difference provides a novel concept in understanding and managing acid–base disturbance in patients. However, its application in pediatrics is limited. This study aimed to evaluate a correlation between the physicochemical approach and blood gas pH for acid–base determination in critically ill pediatric patients.

Results
A total of 130 pediatric patients were included, corresponding to 1338 paired measures for analyses. Of these, the metabolic subgroup (743 paired measures) was defined. Among physicochemical parameters, the effective strong ion difference showed the best correlation with the blood gas pH in the whole cohort (R = 0.398; p < 0.001) and the metabolic subgroup (R = 0.685; p < 0.001). Other physicochemical parameters (i.e., the simplified and the apparent strong ion difference, the strong ion gap, and the sodium chloride gap) and the traditional measures (standard base excess, lactate, chloride and bicarbonate) also showed varying degrees of correlation. This study revealed the positive correlation between physicochemical parameters and the blood gas pH, serving as a connecting dot for further investigations using physicochemical approach to evaluate acid–base disturbance in pediatric population.