bluuebunny/crossref_metadata_2025 huggingface dataset:
Fault diagnosis of motor bearing based on deep learning
Authors: Jian Yifan , Qing Xianguo , He Liang , Zhao Yang , Qi Xiao , Du Ming
Published: September 2019

The effective fault diagnosis of the motor bearings not only can ensure the smooth and efficient operation of equipment but also can detect and eliminate the running fault in time to prevent major accidents. Based on deep learning algorithm, this article constructs a stacked auto-encoder network. The input data are compressed and reduced by introducing sparsity constraint, so that the network can accurately extract the fault characteristics of the input data, and the fault recognition ability of the network can be improved by introducing random noise. The simulation result shows that the stacked auto-encoder network can not only overcome the shortcomings of traditional fault diagnosis method that requires to distinguish fault samples manually and needs a large number of prior knowledge but also realize the self-learning of fault signal feature. The accuracy rate of fault identification reaches 98%, 94%, 96%, and 95.5% in four different working conditions. What’s more, the network can exhibit strong robustness under different working conditions. Finally, the new research ideas of fault diagnosis in thermal power plant are put forward by copying the idea of fault diagnosis of motor bearing.
Note-taking format and difficulty impact learning from instructor-provided lecture notes
Authors: Bellinger David B , DeCaro Marci S
Published: September 2019

The method students use to take notes impacts how they process lecture information. The current experiment examined how the format and amount of content included in instructor-provided notes affect learning. Undergraduate students listened to a brief audio-recorded science lecture that emphasised independent facts, while using one of four note-taking guides. These guides varied in their format (outline notes, cloze notes) and level of difficulty (less-difficult, more-difficult). Outline notes included a partially complete organisational framework, promoting knowledge of relationships among concepts. Cloze notes included all lecture content with select words missing, encouraging processing of specific details. Metacognitive ratings and an objective cognitive load measure confirmed that outline note-taking was the most difficult method. However, outline notes led to higher performance than cloze notes on free recall and inference questions, and equal performance on verbatim questions. These benefits were greatest in the more-difficult outline notes condition, when less information was provided. These findings are consistent with the material-appropriate difficulty framework. Increasing note-taking difficulty was desirable, but only when the activity elicited semantic processing that complemented the type of processing afforded by the learning material.
Testing the independence of self-reported interoceptive accuracy and attention
Authors: Murphy Jennifer , Brewer Rebecca , Plans David , Khalsa Sahib S , Catmur Caroline , Bird Geoffrey
Published: September 2019

It has recently been proposed that measures of the perception of the state of one’s own body (“interoception”) can be categorised as one of several types depending on both how an assessment is obtained (objective measurement vs. self-report) and what is assessed (degree of interoceptive attention vs. accuracy of interoceptive perception). Under this model, a distinction is made between beliefs regarding the degree to which interoceptive signals are the object of attention and beliefs regarding one’s ability to perceive accurately interoceptive signals. This distinction is difficult to test, however, because of the paucity of measures designed to assess self-reported perception of one’s own interoceptive accuracy. This article therefore reports on the development of such a measure, the Interoceptive Accuracy Scale (IAS). Use of this measure enables assessment of the proposed distinction between beliefs regarding attention to, and accuracy in perceiving, interoceptive signals. Across six studies, we report on the development of the IAS and, importantly, its relationship with measures of trait self-reported interoceptive attention, objective interoceptive accuracy, confidence in the accuracy of specific interoceptive percepts, and metacognition with respect to interoceptive accuracy. Results support the distinction between individual differences in perceived attention towards interoceptive information and the accuracy of interoceptive perception.
Improved N-dimensional data visualization from hyper-radial values
Authors: Paciencia Todd , Bihl Trevor , Bauer Kenneth
Published: September 2019

Higher-dimensional data, which is becoming common in many disciplines due to big data problems, are inherently difficult to visualize in a meaningful way. While many visualization methods exist, they are often difficult to interpret, involve multiple plots and overlaid points, or require simultaneous interpretations. This research adapts and extends hyper-radial visualization, a technique used to visualize Pareto fronts in multi-objective optimizations, to become an n-dimensional visualization tool. Hyper-radial visualization is seen to offer many advantages by presenting a low-dimensionality representation of data through easily understood calculations. First, hyper-radial visualization is extended for use with general multivariate data. Second, a method is developed by which to optimally determine groupings of the data for use in hyper-radial visualization to create a meaningful visualization based on class separation and geometric properties. Finally, this optimal visualization is expanded from two to three dimensions in order to support even higher-dimensional data. The utility of this work is illustrated by examples using seven datasets of varying sizes, ranging in dimensionality from Fisher Iris with 150 observations, 4 features, and 3 classes to the Mixed National Institute of Standards and Technology data with 60,000 observations, 717 non-zero features, and 10 classes.
The influence of urban built environment on residential burglary in China: Testing the encounter and enclosure hypotheses
Authors: Yue Han , Zhu Xinyan
Published: September 2019

It is widely recognized that crimes are clustered in space. Features of the built environment are among various factors associated with crime clustering patterns. There are two competing perspectives on this association: the “encounter” and “enclosure” hypotheses. This study examines the effect of the built environment on the spatial distribution of residential burglary in Wuhan, China, aiming to test these two competing perspectives. First, we review existing studies analyzing the influence of the built environment on residential burglary, especially those based on the two hypotheses. We then conduct an exploratory data analysis to observe the spatial and temporal distribution patterns of residential burglaries. Next, we use a multivariate spatial regression model to evaluate the influence of various built environment characteristics on residential burglaries, after controlling for socio-demographic variables, guardianship, and the time-of-day effect. The results suggest a double peak in the hourly distribution of burglaries: 6:00 a.m.–8:59 a.m. and 5:00 p.m.–7:59 p.m. Burglaries are positively and significantly autocorrelated in space and mainly concentrated in the north-west and central areas of Wuhan. Two transport facilities features (intersection density and the presence of subway stations), three building features (multiple stories, high housing prices, and older houses), and land-use mix are each positively correlated with burglary. However, the burglary count is negatively correlated with the ratio of the residential land. Overall, neighborhoods with high permeability are vulnerable to residential burglaries. Thus, the principle of access control promoted by the enclosure hypothesis appears effective in preventing residential crime. The results’ implications for crime prevention and urban design practice are also discussed.
Do early prednisolone and other immunosuppressant therapies prevent generalization in ocular myasthenia gravis in Western populations: a systematic review and meta-analysis
Authors: Li Mingxia , Ge Fangfang , Guo Rongjing , Ruan Zhe , Gao Yanwu , niu Chunxiao , Lin Hong , Zhao Zhengwei , Zhou Yongan , Li Zhuyi , Chang Ting
Published: September 2019

Background:

The majority of ocular myasthenia gravis (OMG) patients will progress to generalized myasthenia gravis (GMG), usually within 2 years of disease onset. The aim of this meta-analysis was to evaluate the effect of early prednisolone and other immunosuppressants therapy on the generalization rate in OMG patients.

Methods:

We searched the CENTRAL, EMBASE, and MEDLINE databases via the Ovid SP database for all relevant publications on 16 July 2018.

Results:

Eight studies comprising a total of 547 participants were included in our meta-analysis. Compared with pyridostigmine treatment, prednisolone and other immunosuppressants therapy produced an odds ratio (OR) for the development of GMG of 0.19 [95% confidence interval (CI), 0.11–0.30; I2 = 37%], indicating that early prednisolone and other immunosuppressants therapy reduced the generalization rate in OMG by 81%.

Conclusions:

Early prednisolone and other immunosuppressants therapy can significantly reduce the risk of generalization in OMG patients, and should be considered in newly diagnosed OMG patients. Due to the inclusion of retrospective studies, this noted effect might have been related to corticosteroids, especially when immunosuppressants used at low dosages and in mild disease. Additionally, the data derived from Western populations, thus a prospective randomized controlled trial (RCT) is warranted to confirm this effect of early prednisolone and other immunosuppressants therapy on OMG generalization both in Western and Asian populations.
Lingual Tonsil Hypertrophy in Patients With Allergic Rhinitis
Authors: Çoban Kübra , Köycü Alper , Aydın Erdinc
Published: September 2019

Background

Lingual tonsils, part of the Waldeyers’ Ring, are located in base of the tongue. They are commonly observed in childhood, due to increased immunological activity. Several factors such as laryngopharyngeal reflux, younger age, smoking, and obesity are associated with hypertrophy of lingual tonsils (LTH) in adulthood. However, the relation between allergic rhinitis and LTH is not clearly highlightened in the literature so far.

Objective

To investigate the role of allergic rhinitis in the development of LTH.

Methods

Adult patients who were diagnosed with allergic rhinitis were included in the study group. The control group consisted of age- and sex-match healthy volunteers. Complete otorhinolaryngology examination including fiberoptic endoscopic evaluation was performed to both groups. Blood samples were obtained for total immunglobulin E levels, and skin prick tests were performed to both groups. Patients with allergy complaints and positive skin prick tests were included in the study group, while healthy volunteers with negative skin prick tests were enrolled in the control group. The grading for LTH was achieved by a physician who was blind to the study.

Results

The incidence of LTH was significantly higher in the study group when compared to the control group ( P = .001). Similarly, the incidence of grade 3 LTH was significantly higher in the study group compared to the controls ( P = .002).

Conclusion

According to our results, LTH is more frequently observed in patients with allergic rhinitis. Grade 3 representing larger LTH is more commonly seen in patients with allergic rhinitis.
Evaluating urban metabolism assessment methods and knowledge transfer between scientists and practitioners: A combined framework for supporting practice-relevant research
Authors: Perrotti Daniela
Published: September 2019

Recent years have seen a substantial growth in urban metabolism research, resulting from increasing scientific consensus that metabolic flow assessments can inform resource-efficient urban policy. However, only a few works report on retrospective evaluation of the relevance and impact of urban metabolism studies in urban planning. Practice-relevant urban metabolism research depends on the applicability of assessment methods as well as on the effectiveness of knowledge transfer between scientists and practitioners. This paper presents a retrospective evaluation of a collaborative urban metabolism project (EU-FP7 BRIDGE) conducted through empirical inquiry. The goal of the inquiry was to evaluate the applicability of the BRIDGE assessment method in urban planning and the effectiveness of the knowledge-transfer approach in one of the BRIDGE case-study cities (Helsinki, Finland) in a combined fashion. Through generalization of key findings on strengths and areas of improvement, a combined framework to evaluate both aspects in the design of urban metabolism projects is proposed. The framework aims at supporting scientists and practitioners in the development of collaborative research that can accommodate expectations as well as sustainability priorities and objectives of both parties.
Statistical distribution of building lot depth: Theoretical and empirical investigation of downtown districts in Tokyo
Authors: Usui Hiroyuki
Published: September 2019

A building lot represents one of the most important basic spatial objects of urban form because building lots are basically adjacent to road networks and combine to make an exact whole with no leftover space. Thus, it is important to understand the relationship between the sizes and shapes of building lots and the density of buildings and road networks at a district scale. While building lot sizes and frontages are known to follow a log-normal distribution, respectively, the probability density function that building lot depths follow remains uncertain. Therefore, the research objective is to answer the following research question: What types of statistical distribution of building lot depths are found if the values of building density (the number of buildings per unit area) and road network density (total lengths of road networks per unit area) are given at a district scale? Assuming that (A1) one building lot has one building; (A2) building lot depth is defined as the ratio of building lot size to frontage; and (A3) building lot frontages and depths are independently distributed, I derived the probability density function of rectangular building lot depths as a log-normal distribution. As the result of theoretical investigations, it was found that (1) the probability density function of building lot depths depends not on the building density but on road network density; and (2) it depends not only on road network density but also on the variation in building lot sizes and frontages. For the empirical study of 20 downtown districts of the Tokyo metropolitan region, I tested (A3) and the log-normality of building lot depths and applied the derived function. At a 5% significance level, it was found that the hypothesis of log-normality of building lot depths was accepted in 12 of the 20 selected districts. These findings imply that when we discuss the criteria of the variation in building lot sizes and frontages, we must take into consideration the variation in building lot depths and vice versa. I also derived the probability density function of building setbacks, whose parameters include road network density and building coverage ratio. These findings are expected to provide urban planners with a theoretical basis to not only reconsider the validity of the present road network density and building coverage ratio (form-based codes) but to additionally discuss the relationship between building-lot-scale and district-scale urban physical planning.
Magnetization Dynamics Modulated by Dzyaloshinskii-Moriya Interaction in the Double-Interface Spin-Transfer Torque Magnetic Tunnel Junction
Authors: Li Simin , Wang Zhaohao , Wang Yijie , Wang Mengxing , Zhao Weisheng
Published: September 2019

Currently double-interface magnetic tunnel junctions (MTJs) have been developed for enhancing the thermal stability barrier at the nanoscale technology node. Dzyaloshinskii–Moriya interaction (DMI) inevitably exists in such devices due to the use of the heavy-metal/ferromagnet structures. Previous studies have demonstrated the detrimental effect of DMI on the conventional single-interface spin-transfer torque (STT) MTJs. Here, in this work, we will prove that the detrimental effect of DMI could be almost eliminated in the double-interface STT-MTJ. This conclusion is attributed to the suppressing effect of Ruderman–Kittel–Kasuya–Yosida (RKKY) interaction on the DMI. Detailed mechanisms are analyzed based on the theoretical models and micromagnetic simulation results. Our work highlights the importance of appropriately controlling the DMI in the composite free layer of the double-interface STT-MTJ.
Health risk assessments of arsenic and toxic heavy metal exposure in drinking water in northeast Iran
Authors: Alidadi Hosein , Tavakoly Sany Seyedeh Belin , Zarif Garaati Oftadeh Batoul , Mohamad Tafaghodi , Shamszade Hosein , Fakhari Maryam
Published: September 2019

Background

Arsenic and heavy metals are the main cause of water pollution and impact human health worldwide. Therefore, this study aims to assess the probable health risk (non-carcinogenic and carcinogenic risk) for adults and children that are exposed to arsenic and toxic heavy metals (Pb, Ni, Cr, and Hg) through ingestion and dermal contact with drinking water.

Method

In this study, chemical analysis and testing were conducted on 140 water samples taken from treated drinking water in Mashhad, Iran. The health risk assessments were evaluated using hazard quotient (HQ), hazard index (HI), and lifetime cancer risk (CR).

Results

The results of the HQ values of arsenic and heavy metals for combined pathways were below the safety level (HQ < 1) for adults, while the HI for children were higher than the safety limit in some stations. Likewise, Cr showed the highest average contribution of HItotal elements (55 to 71.2%) for adult and children population. The average values of total carcinogenic risk (TCR) through exposure to drinking water for children and adults were 1.33 × 10−4 and 7.38 × 10−5, respectively.

Conclusion

Overall, the CRtotal through exposure to drinking water for children and adults was borderline or higher than the safety level of US EPA risk, suggesting the probability of carcinogenic risk for the children and adults to the carcinogenic elements via ingestion and dermal routes. Therefore, appropriate purification improvement programs and control measures should be implemented to protect the health of the residents in this metropolitan city.
Decision-making under uncertainty in environmental health policy: new approaches
Authors: Reis Jacques , Spencer Peter S.
Published: September 2019

Decision-making in environmental health policy is a complex procedure even in well-known conditions. Thus, in the case of uncertainty, decision-making becomes a hurdle race. We address scientific uncertainty, methods to reduce uncertainty, biomedical doubt and science communication, and the role of stakeholders, activists, lobbies and media that together influence policy decisions. We also consider the major responsibility and role of the medico-scientific community in this process. This community can and should teach the principle of scientific uncertainty to all stakeholders, advise policy-makers and underline the ethical issues, considering that our brains are not only the deposit of our humanity but also the route to environmental health and societal harmony.
Identifying protein complexes based on an edge weight algorithm and core-attachment structure
Authors: Wang Rongquan , Liu Guixia , Wang Caixia
Published: September 2019

Background

Protein complex identification from protein-protein interaction (PPI) networks is crucial for understanding cellular organization principles and functional mechanisms. In recent decades, numerous computational methods have been proposed to identify protein complexes. However, most of the current state-of-the-art studies still have some challenges to resolve, including their high false-positives rates, incapability of identifying overlapping complexes, lack of consideration for the inherent organization within protein complexes, and absence of some biological attachment proteins.

Results

In this paper, to overcome these limitations, we present a protein complex identification method based on an edge weight method and core-attachment structure (EWCA) which consists of a complex core and some sparse attachment proteins. First, we propose a new weighting method to assess the reliability of interactions. Second, we identify protein complex cores by using the structural similarity between a seed and its direct neighbors. Third, we introduce a new method to detect attachment proteins that is able to distinguish and identify peripheral proteins and overlapping proteins. Finally, we bind attachment proteins to their corresponding complex cores to form protein complexes and discard redundant protein complexes. The experimental results indicate that EWCA outperforms existing state-of-the-art methods in terms of both accuracy andp-value. Furthermore, EWCA could identify many more protein complexes with statistical significance. Additionally, EWCA could have better balance accuracy and efficiency than some state-of-the-art methods with high accuracy.

Conclusions

In summary, EWCA has better performance for protein complex identification by a comprehensive comparison with twelve algorithms in terms of different evaluation metrics. The datasets and software are freely available for academic research athttps://github.com/RongquanWang/EWCA.
A purely bioinformatic pipeline for the prediction of mammalian odorant receptor gene enhancers
Authors: Degl’Innocenti Andrea , Meloni Gabriella , Mazzolai Barbara , Ciofani Gianni
Published: September 2019

Background

In most mammals, a vast array of genes coding for chemosensory receptors mediates olfaction. Odorant receptor (OR) genes generally constitute the largest multifamily (> 1100 intact members in the mouse). From the whole pool, each olfactory neuron expresses a single OR allele following poorly characterized mechanisms termed OR gene choice. OR genes are found in genomic aggregations known as clusters. Nearby enhancers, named elements, are crucial regulators of OR gene choice. Despite their importance, searching for new elements is burdensome. Other chemosensory receptor genes responsible for smell adhere to expression modalities resembling OR gene choice, and are arranged in genomic clusters — often with chromosomal linkage to OR genes. Still, no elements are known for them.

Results

Here we present an inexpensive framework aimed at predicting elements. We redefine cluster identity by focusing on multiple receptor gene families at once, and exemplify thirty — not necessarily OR-exclusive — novel candidate enhancers.

Conclusions

The pipeline we introduce could guide future in vivo work aimed at discovering/validating new elements. In addition, our study provides an updated and comprehensive classification of all genomic loci responsible for the transduction of olfactory signals in mammals.
Towards pixel-to-pixel deep nucleus detection in microscopy images
Authors: Xing Fuyong , Xie Yuanpu , Shi Xiaoshuang , Chen Pingjun , Zhang Zizhao , Yang Lin
Published: September 2019

Background

Nucleus or cell detection is a fundamental task in microscopy image analysis and supports many other quantitative studies such as object counting, segmentation, tracking, etc. Deep neural networks are emerging as a powerful tool for biomedical image computing; in particular, convolutional neural networks have been widely applied to nucleus/cell detection in microscopy images. However, almost all models are tailored for specific datasets and their applicability to other microscopy image data remains unknown. Some existing studies casually learn and evaluate deep neural networks on multiple microscopy datasets, but there are still several critical, open questions to be addressed.

Results

We analyze the applicability of deep modelsspecificallyfor nucleus detection across a wide variety of microscopy image data. More specifically, we present a fully convolutional network-based regression model and extensively evaluate it on large-scale digital pathology and microscopy image datasets, which consist of 23 organs (or cancer diseases) and come from multiple institutions. We demonstrate that for a specific target dataset, training with images from the same types of organs might be usually necessary for nucleus detection. Although the images can be visually similar due to the same staining technique and imaging protocol, deep models learned with images from different organs might not deliver desirable results and would require model fine-tuning to be on a par with those trained with target data. We also observe that training with a mixture of target and other/non-target data does not always mean a higher accuracy of nucleus detection, and it might require proper data manipulation during model training to achieve good performance.

Conclusions

We conduct a systematic case study on deep models for nucleus detection in a wide variety of microscopy images, aiming to address several important but previously understudied questions. We present and extensively evaluate an end-to-end, pixel-to-pixel fully convolutional regression network and report a few significant findings, some of which might have not been reported in previous studies. The model performance analysis and observations would be helpful to nucleus detection in microscopy images.
Biological variation of immunological blood biomarkers in healthy individuals and quality goals for biomarker tests
Authors: Aziz Najib , Detels Roger , Quint Joshua J. , Gjertson David , Ryner Timothy , Butch Anthony W.
Published: September 2019

Background

Cytokines, chemokines, adipocytokines, soluble cell receptors, and immune activation markers play an important role in immune responsiveness and can provide prognostic value since they reflect underlying conditions and disease states. This study was undertaken to investigate the components of biological variation for various laboratory tests of blood immunological biomarkers.

Results

Estimates of intra-individual coefficient of variation (CVI) and inter-individual coefficient of variation (CVG) were examined for blood immunological biomarkers. Biomarkers with CVI < 10% for both genders were CD3, CD4, and CD8 T-cells, serum levels of soluble cluster of differentiation 14 (sCD14), sCD163, and soluble glycoprotein 130 (sgp130). The CVIfor serum levels of adiponectin, interleukin-1 receptor antagonist (IL-1Ra), macrophage inflammatory protein 1 beta (MIP-1β), soluble CD40 Ligand (sCD40L), soluble interleukin-2 receptor alpha (sIL-2Rα), soluble interleukin-6 receptor (sIL-6R), soluble tumor necrosis factor receptor II (sTNF-RII), and tumor necrosis factor alpha (TNF-α) were between 11 and 20%. Biomarkers with CVG < 20% were CD3 T-cell, and serum concentrations of sCD14, sCD40L, and sgp130. The biomarkers with CVG > 40% were adiponectin, IL-1ra, leptin, MIP-1β, sCD163, and sIL-2Rα.

Conclusion

The biological variations of biomarkers have important monitoring value for longitudinal investigation and are essential for quality specification of tests that are performed in the laboratory. The CVIwas relatively small while CVGwas comparatively large and mean values of each biomarker vary between subjects. The individuality of biomarkers significantly influences reference interval values. A majority of the biomarkers in this study had strong individuality and the result of each biomarker should be cautiously interpreted if using established reference interval values. Comparison of a patient’s test result with previous ones may be more useful than the usage of conventional reference values.
Genome wide search to identify reference genes candidates for gene expression analysis in Gossypium hirsutum
Authors: Smitha P. K. , Vishnupriyan K. , Kar Ananya S. , Anil Kumar M. , Bathula Christopher , Chandrashekara K. N. , Dhar Sujan K. , Das Manjula
Published: September 2019

Background

Cotton is one of the most important commercial crops as the source of natural fiber, oil and fodder. To protect it from harmful pest populations number of newer transgenic lines have been developed. For quick expression checks in successful agriculture qPCR (quantitative polymerase chain reaction) have become extremely popular. The selection of appropriate reference genes plays a critical role in the outcome of such experiments as the method quantifies expression of the target gene in comparison with the reference. Traditionally most commonly used reference genes are the “house-keeping genes”, involved in basic cellular processes. However, expression levels of such genes often vary in response to experimental conditions, forcing the researchers to validate the reference genes for every experimental platform. This study presents a data science driven unbiased genome-wide search for the selection of reference genes by assessing variation of > 50,000 genes in a publicly available RNA-seq dataset of cotton species Gossypium hirsutum.

Result

Five genes (TMN5, TBL6, UTR5B, AT1g65240 and CYP76B6) identified by data-science driven analysis, along with two commonly used reference genes found in literature (PP2A1 and UBQ14) were taken through qPCR in a set of 33 experimental samples consisting of different tissues (leaves, square, stem and root), different stages of leaf (young and mature) and square development (small, medium and large) in both transgenic and non-transgenic plants. Expression stability of the genes was evaluated using four algorithms - geNorm, BestKeeper, NormFinder and RefFinder.

Conclusion

Based on the results we recommend the usage of TMN5 and TBL6 as the optimal candidate reference genes in qPCR experiments with normal and transgenic cotton plant tissues. AT1g65240 and PP2A1 can also be used if expression study includes squares. This study, for the first time successfully displays a data science driven genome-wide search method followed by experimental validation as a method of choice for selection of stable reference genes over the selection based on function alone.
Transcriptional regulation of stilbene synthases in grapevine germplasm differentially susceptible to downy mildew
Authors: Ciaffi Mario , Paolacci Anna Rita , Paolocci Marco , Alicandri Enrica , Bigini Valentina , Badiani Maurizio , Muganu Massimo
Published: September 2019

Background

To limit the impact of the downy mildew disease of grapevine and reduce the need to recur to chemical treatments, an effective strategy might be recovering adaptive resistance traits in both cultivated and wildV. viniferagermplasm.Considering that stilbenes represent the most important class of phytoalexins in theVitaceae, the constitutive expression and transcriptional activation of all the functional members of the stilbene synthase gene family were analysed in a group of nine grapevine genotypes following artificial infection with the oomycetePlasmopara viticola, the causal agent of the disease. In addition, in the same genotypes we analyzed the expression of genes encoding for two transcription factors involved in the transcriptional regulation of the stilbene synthase genes, namelyVvMYB14andVvMYB15, and of genes encoding for chalcone synthases.

Results

Downy mildew incidence and severity ranged from nihil to high in the grapevine genotypes considered, being low to moderate in a subgroup ofV. viniferagenotypes. The constitutive expression of the stilbene synthase genes as well as the extent of their transcriptional activation followingP. viticolainoculation appeared to be inversely related to the proneness to develop disease symptoms upon infection. In a specular manner, followingP. viticolainoculation all the chalcone synthase genes were up-regulated in the susceptible grapevine genotypes and down-regulated in the resistant ones. The infection brought byP. viticolaappeared to elicit a co-ordinated and sequential transcriptional activation of distinct stilbene synthase genes subsets, each of which may be regulated by a distinct and specific MYB transcription factor.

Conclusions

The present results suggest that the induction of stilbene biosynthesis may contribute to the basal immunity against the downy mildew of grapevine, thus representing an adaptive resistance trait to recover, in both cultivated and wildV. viniferagermplasm. During the early stages ofP. viticolainfection, an antagonistic interaction between flavonol and stilbene biosynthesis might occur, whose outcome might determine the subsequent extent of disease symptoms. Further studies are needed to decipher the possible regulatory mechanisms involved in the antagonistic crosstalk between these two metabolic pathways in resistant and susceptible genotypes in response toP. viticola.
Apolipoprotein E gene polymorphism and the risk of cardiovascular disease and type 2 diabetes
Authors: Liu Sudong , Liu Jing , Weng Ruiqiang , Gu Xiaodong , Zhong Zhixiong
Published: September 2019

Background

The role of apolipoprotein E gene (APOE) in lipid metabolism has been well established, and APOE is associated with the risk of cardiovascular disease (CVD) and diabetes mellitus (DM). However, the relationship between APOE polymorphisms and type 2 diabetes (T2DM) with or without CVD remains unclear.

Methods

In this cross-sectional study, a total of 924 participants including 211 controls (CVD-T2DM-), 247 T2DM patients with CVD (CVD-T2DM+), 232 CVD patients without T2DM (CVD + T2DM-) and 234 T2DM patients with CVD (CVD + T2DM+), were genotyped using chip platform. The association between APOE polymorphisms and T2DM patients with or without CVD was analyzed by univariable and multivariable logistic analysis.

Results

The present study showed that the frequency of E3/E4 increased in T2DM patients with CVD (p < 0.01). The ε4 allele was higher in CVD patients without T2DM (p < 0.01) and T2DM patients with CVD (p < 0.01) as compared with the controls.

Conclusions

The subjects carrying ε4 allele have increased risk of CVD and T2DM, and exhibit higher level of lipid profiles.
A rare case of Colistin-resistant Salmonella Enteritidis meningitis in an HIV-seropositive patient
Authors: Rule Roxanne , Mbelle Nontombi , Sekyere John Osei , Kock Marleen , Hoosen Anwar , Said Mohamed
Published: September 2019

Background

Non-typhoidal salmonellae (NTS) have been associated with invasive disease, notably meningitis, in immunocompromised individuals. Infections of this nature carry high rates of morbidity and mortality. Colistin resistance in salmonellae is a rare finding, more so in an invasive isolate such as cerebrospinal fluid (CSF). Colistin resistance has important infection control implications and failure to manage this phenomenon may lead to the loss of our last line of defence against multi-drug resistant Gram-negative organisms. To our knowledge, this is the first reported clinical case of colistin-resistant Salmonella Enteritidis meningitis in South Africa.

Case presentation

We report a case of a young male patient with advanced human immunodeficiency virus (HIV) infection who presented to hospital with symptoms of meningitis. Cerebrospinal fluid (CSF) cultured a Salmonella Enteritidis strain. Antimicrobial susceptibility testing (AST) of the isolate, revealed the strain to be colistin resistant. Despite early and aggressive antimicrobial therapy, the patient succumbed to the illness after a short stay in hospital. Subsequent genomic analysis of the isolate showed no presence of the mcr genes or resistance-conferring mutations in phoPQ, pmrAB, pmrHFIJKLME/arnBCADTEF, mgrB, and acrAB genes, suggesting the presence of a novel colistin resistance mechanism.

Conclusion

Invasive non-typhoidal salmonellae infection should be suspected in patients with advanced immunosuppression who present with clinical features of meningitis. Despite early and appropriate empiric therapy, these infections are commonly associated with adverse outcomes to the patient. Combination therapy with two active anti-Salmonella agents may be a consideration in the future to overcome the high mortality associated with NTS meningitis. Colistin resistance in clinical Salmonella isolates, although a rare finding at present, has significant public health and infection control implications. The causative mechanism of resistance should be sought in all cases.
“Enterocytozoon bieneusi and Cryptosporidium: a cross-sectional study conducted throughout Thailand”
Authors: Prasertbun Rapeepun , Mori Hirotake , Sukthana Yaowalark , Popruk Supaluk , Kusolsuk Teera , Hagiwara Katsuro , Mahittikorn Aongart
Published: September 2019

Background

Enterocytozoon bieneusi and Cryptosporidium spp. are prevalent zoonotic parasites associated with a high burden among children. To date only limited molecular epidemiological data on E. bieneusi and Cryptosporidium spp. in humans living in Thailand has been published.

Methods

PCR-based tools were used to detect and characterize E. bieneusi and Cryptosporidium spp. The internal transcribed spacer (ITS) region of the rRNA gene was used to investigate E. bieneusi, and the small subunit (SSU) rRNA gene was used to investigate Cryptosporidium spp., and 697 fecal samples from villagers and school children in rural areas in Thailand were analyzed.

Results

The infection rates were 2.15% (15/697) for E. bieneusi and 0.14% (1/697) for Cryptosporidium spp. The prevalence of E. bieneusi was significantly high in Loei province. Sequence analysis indicated that the Cryptosporidium isolate was C. parvum. Nine E. bieneusi genotypes were identified, EbpC, Peru12, TMH6, TMH3, TMH7, H, D, and two novel genotypes TMLH1 and TMLH2. E. bieneusi prevalence was significantly higher in male participants than in female participants, and in children aged 3–15 years than in participants aged > 15 years.

Conclusions

The prevalence, genotypes, and zoonotic potential of E. bieneusi were found to vary significantly high even in one country. Transmission routes and key animal carriers of E. bieneusi may be associated with differences in hygiene, sanitation, and cultural behaviors. Further molecular studies including longitudinal studies will be required to unveil epidemiological characteristics of these opportunistic intestinal protozoa in all over the countries.
Molecular mechanisms of hydrogen sulfide against uremic accelerated atherosclerosis through cPKCβII/Akt signal pathway
Authors: Xiong Ruifang , Lu Xiangxue , Song Jinghong , Li Han , Wang Shixiang
Published: September 2019

Background

Cardiovascular disease is the most common complication and leading cause of death in maintenance hemodialysis patients. The protection mechanism of hydrogen sulfide (H2S) and the specific role of conventional protein kinase C βII (cPKCβII)/Akt signaling pathway in the formation of atherosclerosis is still controversial.

Methods

8-week-old male ApoE−/− mice were treated with 5/6 nephrectomy and high-fat diet to make uremia accelerated atherosclerosis (UAAS) model. Mice were divided into normal control group (control group), sham operation group (sham group), UAAS group, L-cysteine group (UAAS+L-cys group), sodium hydrosulfide group (UAAS+NaHS group), and propargylglycine group (UAAS+PPG group). Western blot was used to detect cPKCβII activation, Akt phosphorylation and endothelial nitric oxide synthase (eNOS) expression in mice aorta.

Results

The membrane translocation of cPKCβII in UAAS group was higher than sham group, and L-cys or NaHS injection could suppress the membrane translocation, but PPG treatment resulted in more membrane translocation of cPKCβII (P < 0.05, n = 6 per group). Akt phosphorylation and the eNOS expression in UAAS group was lower than sham group, and L-cys or NaHS injection could suppress the degradation of Akt phosphorylation and the eNOS expression, but PPG treatment resulted in more decrease in the Akt phosphorylation and the eNOS expression (P < 0.05, n = 6 per group).

Conclusion

Endogenous cystathionine-γ-lyase (CSE)/H2S system protected against the formation of UAAS via cPKCβII/Akt signal pathway. The imbalance of CSE/H2S system may participate in the formation of UAAS by affecting the expression of downstream molecule eNOS, which may be mediated by cPKCβII/Akt signaling pathway.
Lab-based and diagnosis-based chronic kidney disease recognition and staging concordance
Authors: Diamantidis Clarissa J. , Hale Sarah L. , Wang Virginia , Smith Valerie A. , Scholle Sarah Hudson , Maciejewski Matthew L.
Published: September 2019

Background

Chronic kidney disease (CKD) is often under-recognized and poorly documented via diagnoses, but the extent of under-recognition is not well understood among Medicare beneficiaries. The current study used claims-based diagnosis and lab data to examine patient factors associated with clinically recognized CKD and CKD stage concordance between claims- and lab-based sources in a cohort of Medicare beneficiaries.

Methods

In a cohort of fee-for-service (FFS) beneficiaries with CKD based on 2011 labs, we examined the proportion with clinically recognized CKD via diagnoses and factors associated with clinical recognition in logistic regression. In the subset of beneficiaries with CKD stage identified from both labs and diagnoses, we examined concordance in CKD stage from both sources, and factors independently associated with CKD stage concordance in logistic regression.

Results

Among the subset of 206,036 beneficiaries with lab-based CKD, only 11.8% (n = 24,286) had clinically recognized CKD via diagnoses. Clinical recognition was more likely for beneficiaries who had higher CKD stages, were non-elderly, were Hispanic or non-Hispanic Black, lived in core metropolitan areas, had multiple chronic conditions or outpatient visits in 2010, or saw a nephrologist. In the subset of 18,749 beneficiaries with CKD stage identified from both labs and diagnoses, 70.0% had concordant CKD stage, which was more likely if beneficiaries were older adults, male, lived in micropolitan areas instead of non-core areas, or saw a nephrologist.

Conclusions

There is significant under-diagnosis of CKD in Medicare FFS beneficiaries, which can be addressed with the availability of lab results.
Tumor-infiltrating CD8+ T cells combined with tumor-associated CD68+ macrophages predict postoperative prognosis and adjuvant chemotherapy benefit in resected gastric cancer
Authors: Lu Jun , Xu Yu , Wu Yuan , Huang Xiao-yan , Xie Jian-wei , Wang Jia-bin , Lin Jian-xian , Li Ping , Zheng Chao-hui , Huang Ai-min , Huang Chang-ming
Published: September 2019

Background

Tumor-infiltrating immune cells are present in various malignant tumors, but their clinical significance in gastric cancer (GC) remains unclear. This study aimed to investigate the prognostic significance of tumor-infiltrating lymphocytes (TILs) and tumor-associated macrophages (TAMs).

Methods

Using a prospective database containing 401 cases of GC, we evaluated TIL (cluster of differentiation 8 (CD8) expression) and TAM (cluster of differentiation 68 (CD68) expression) statuses via immunohistochemical staining.

Results

Compared with CD8+ TIL-negative cases (n = 196, 48.6%), CD8+ TIL-positive cases (n = 205, 51.1%) showed significantly better recurrence-free survival (RFS) [log-rank p<0.001; multivariate HR: 0.372; 95% confidence interval (CI): 0.239–0.579, p<0.001]. In contrast, compared with CD68+ TAM-negative cases (n = 217, 54.1%), CD68+ TAM-positive cases (n = 184, 45.9%) had significantly poor RFS [log-rank p<0.001; multivariate HR: 2.182; 95% CI: 1.435–3.318, p<0.001]. Thus, patients with a positive CD8+ TIL and negative CD68+ TAM status exhibited significantly increased RFS. Multivariate analysis demonstrated that CD8+ TILs and CD68+ TAMs may serve as independent prognostic markers for RFS. Incorporating CD8+ TIL and CD68+ TAM statuses into the AJCC TNM system generated a predictive model with better predictive accuracy for RFS. More importantly, patients with a positive TIL and negative TAM status showed a tendency of improved RFS after postoperative adjuvant chemotherapy (PAC). Similar results were obtained by overall survival (OS) analysis.

Conclusions

CD8+ TIL and CD68+ TAM statuses were identified as independent prognostic factors that may be integrated into the current TNM staging system to refine risk stratification and to better predict the survival benefit from PAC in patients with GC.

Trial registration

The current controlled trial was registered at ClinicalTrials.gov (ID: NCT02327481) on December 30, 2014.
Lentivirus-mediated CDglyTK gene-modified free flaps by intra-artery perfusion show targeted therapeutic efficacy in rat model of breast cancer
Authors: Zhang Jianhua , Liu Yuanbo , Zang Mengqing , Zhu Shan , Chen Bo , Li Shanshan , Xue Bingjian , Yan Li
Published: September 2019

Background

Free flap-mediated gene therapy in the tumor bed following surgical resection is a promising approach in cancer targeted treatment of residual disease. We investigated the selective killing efficacy of a lentivirus-mediated cytosine deaminase-thymidine kinase (CDglyTK) gene in transplanted breast cancer delivered into a free flap by intra-artery perfusion.

Methods

Proliferation, apoptosis, and cell cycle of rat SHZ-88 breast cancer cells transfected with a lentivirus-mediated CD/TK gene were measured following treatment with ganciclovir and 5-flucytosine in vitro. A model of residual disease of breast cancer in a rat superficial inferior epigastric artery (SIEA) flap model was used to study the therapeutic potential of a double suicide CD/TK and prodrug system in vivo.

Results

Killing efficacy of the double suicide CD/TK and prodrug system on SHZ-88 cells was mediated by increased apoptosis and cell cycle arrest at the G1 phase with significant bystander effect. Following recombinant lentivirus transfection of rat SIEA flap by intra-artery perfusion, CD/TK gene expression was limited to the flap, and the volume and weight of transplanted tumors were significantly reduced without observable toxicity.

Conclusions

SIEA flaps transfected with a lentivirus-mediated CDglyTK gene by intra-artery perfusion effectively suppress transplanted breast tumor growth without obvious systemic toxic effects in rats.