bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrating network topology, gene expression data and GO annotation information for protein complex prediction
Authors: Zhang Wei , Xu Jia , Li Yuanyuan , Zou Xiufen
Published: October 2018

The prediction of protein complexes based on the protein interaction network is a fundamental task for the understanding of cellular life as well as the mechanisms underlying complex disease. A great number of methods have been developed to predict protein complexes based on protein–protein interaction (PPI) networks in recent years. However, because the high throughput data obtained from experimental biotechnology are incomplete, and usually contain a large number of spurious interactions, most of the network-based protein complex identification methods are sensitive to the reliability of the PPI network. In this paper, we propose a new method, Identification of Protein Complex based on Refined Protein Interaction Network (IPC-RPIN), which integrates the topology, gene expression profiles and GO functional annotation information to predict protein complexes from the reconstructed networks. To demonstrate the performance of the IPC-RPIN method, we evaluated the IPC-RPIN on three PPI networks of Saccharomycescerevisiae and compared it with four state-of-the-art methods. The simulation results show that the IPC-RPIN achieved a better result than the other methods on most of the measurements and is able to discover small protein complexes which have traditionally been neglected.
Tomographic analysis of the de Sitter model in quantum and classical cosmology
Authors: Stornaiolo Cosimo
Published: October 2018

The importance of the tomographic approach is that either in quantum mechanics as in classical mechanics the state of a physical system is expressed with marginal probability functions called tomograms. The extension of this procedure to quantum cosmology is straightforward. But in this paper, instead of using the tomographic representation, we use tomograms to analyze the properties of the quantum and classical universes, starting from the wave functions in quantum cosmology and from the phase space distributions in classical cosmology. In this, there is a part where we resume the properties of the tomograms. Then, we apply them to study and discuss the properties of the initial conditions introduced by Hartle and Hawking, Vilenkin and Linde and finally we argue about their classical transition. According to the results of this paper it follows that the decay of the cosmological constant from the Planck scale to the present one could be responsible for the transition of the quantum universe to the classical one.
Arbitrary amplitude femtosecond pulse shaping via a digital micromirror device
Authors: Gu Chenglin , Zhang Dapeng , Chang Yina , Chen Shih-Chi
Published: October 2018

An ultrafast spectrum programmable femtosecond laser may enhance the performance of a wide variety of scientific applications, e.g., multi-photon imaging. In this paper, we report a digital micromirror device (DMD)-based ultrafast pulse shaper, i.e., DUPS, for femtosecond laser arbitrary amplitude shaping — the first time a programmable binary device reported to shape the amplitudes of ultrafast pulses spectrum at up to 32[Formula: see text]kHz rate over a broad wavelength range. The DUPS is highly efficient, compact, and low cost based on the use of a DMD in combination with a transmission grating. Spatial and temporal dispersion introduced by the DUPS is compensated by a quasi-4-f setup and a grating pair, respectively. Femtosecond pulses with arbitrary spectrum shapes, including rectangular, sawtooth, triangular, double-pulse, and exponential profile, have been demonstrated in our experiments. A feedback operation process is implemented in the DUPS to ensure a robust and repeatable shaping process. The total efficiency of the DUPS for amplitude shaping is measured to be 27%.
Whole-Genome Alignment and Comparative Annotation
Authors: Armstrong Joel , Fiddes Ian T. , Diekhans Mark , Paten Benedict
Published: October 2018

Rapidly improving sequencing technology coupled with computational developments in sequence assembly are making reference-quality genome assembly economical. Hundreds of vertebrate genome assemblies are now publicly available, and projects are being proposed to sequence thousands of additional species in the next few years. Such dense sampling of the tree of life should give an unprecedented new understanding of evolution and allow a detailed determination of the events that led to the wealth of biodiversity around us. To gain this knowledge, these new genomes must be compared through genome alignment (at the sequence level) and comparative annotation (at the gene level). However, different alignment and annotation methods have different characteristics; before starting a comparative genomics analysis, it is important to understand the nature of, and biases and limitations inherent in, the chosen methods. This review is intended to act as a technical but high-level overview of the field that should provide this understanding. We briefly survey the state of the genome alignment and comparative annotation fields and potential future directions for these fields in a new, large-scale era of comparative genomics.
CRISPR Correction of Duchenne Muscular Dystrophy
Authors: Min Yi-Li , Bassel-Duby Rhonda , Olson Eric N.
Published: October 2018

The ability to efficiently modify the genome using CRISPR technology has rapidly revolutionized biology and genetics and will soon transform medicine. Duchenne muscular dystrophy (DMD) represents one of the first monogenic disorders that has been investigated with respect to CRISPR-mediated correction of causal genetic mutations. DMD results from mutations in the gene encoding dystrophin, a scaffolding protein that maintains the integrity of striated muscles. Thousands of different dystrophin mutations have been identified in DMD patients, who suffer from a loss of ambulation followed by respiratory insufficiency, heart failure, and death by the third decade of life. Using CRISPR to bypass DMD mutations, dystrophin expression has been efficiently restored in human cells and mouse models of DMD. Here, we review recent progress toward the development of possible CRISPR therapies for DMD and highlight opportunities and potential obstacles in attaining this goal.
Systems-Wide Approaches in Induced Pluripotent Stem Cell Models
Authors: Lau Edward , Paik David T. , Wu Joseph C.
Published: October 2018

Human induced pluripotent stem cells (iPSCs) provide a renewable supply of patient-specific and tissue-specific cells for cellular and molecular studies of disease mechanisms. Combined with advances in various omics technologies, iPSC models can be used to profile the expression of genes, transcripts, proteins, and metabolites in relevant tissues. In the past 2 years, large panels of iPSC lines have been derived from hundreds of genetically heterogeneous individuals, further enabling genome-wide mapping to identify coexpression networks and elucidate gene regulatory networks. Here, we review recent developments in omics profiling of various molecular phenotypes and the emergence of human iPSCs as a systems biology model of human diseases.
Cardioprotection during ischemia by coronary collateral growth
Authors: Jamaiyar Anurag , Juguilon Cody , Dong Feng , Cumpston Devan , Enrick Molly , Chilian William M. , Yin Liya
Published: October 2018

Ischemic heart diseases (IHD) cause millions of deaths around the world annually. While surgical and pharmacological interventions are commonly used to treat patients with IHD, their efficacy varies from patient to patient and is limited by the severity of the disease. One promising, at least theoretically, approach for treating IHD is induction of coronary collateral growth (CCG). Coronary collaterals are arteriole-to-arteriole anastomoses that can undergo expansion and remodeling in the setting of coronary disease when the disease elicits myocardial ischemia and creates a pressure difference across the collateral vessel that creates unidirectional flow. Well-developed collaterals can restore blood flow in the ischemic area of the myocardium and protect the myocardium at risk. Moreover, such collaterals are correlated to reduced mortality and infarct size and better cardiac function during occlusion of coronary arteries. Therefore, understanding the process of CCG is highly important as a potentially viable treatment of IHD. While there are several excellent review articles on this topic, this review will provide a unified overview of the various aspects related to CCG as well as an update of the advancements in the field. We also call for more detailed studies with an interdisciplinary approach to advance our knowledge of CCG. In this review, we will describe growth of coronary collaterals, the various factors that contribute to CCG, animal models used to study CCG, and the cardioprotective effects of coronary collaterals during ischemia. We will also discuss the impairment of CCG in metabolic syndrome and the therapeutic potentials of CCG in IHD.
SIRT1-mediated HMGB1 deacetylation suppresses sepsis-associated acute kidney injury
Authors: Wei Siwei , Gao Youguang , Dai Xingui , Fu Weijun , Cai Shumin , Fang Haihong , Zeng Zhenhua , Chen Zhongqing
Published: October 2018

Sepsis is the leading cause of death in the intensive care unit and continues to lack effective treatment. It is widely accepted that high-mobility group box 1 (HMGB1) is a key inflammatory mediator in the pathogenesis of sepsis. Moreover, some studies indicate that the functions of HMGB1 depend on its molecular localization and posttranslational modifications. Our previous study confirms that sirtuin 1, silent information regulator 2-related enzyme 1 (SIRT1), a type III deacetylase, can ameliorate sepsis-associated acute kidney injury (SA-AKI). We explored the effect and mechanism of SIRT1 on HMGB1 using a mouse model of cecal ligation and puncture-induced sepsis and LPS-treated human kidney (HK-2) cell line. We found that HMGB1 is elevated in the serum but is gradually reduced in kidney cells in the later stages of septic mice. The acetylation modification of HMGB1 is a key process before its nucleus-to-cytoplasm translocation and extracellular secretion in kidney cells, accelerating the development of SA-AKI. Moreover, SIRT1 can physically interact with HMGB1 at the deacetylated lysine sites K28, K29, and K30, subsequently suppressing downstream inflammatory signaling. Thus the SIRT1-HMGB1 signaling pathway is a crucial mechanism in the development of SA-AKI and presents a novel experimental perspective for future SA-AKI research.
The determinants, biomarkers, and consequences of microvascular injury in kidney transplant recipients
Authors: Doreille Alice , Dieudé Mélanie , Cardinal Heloise
Published: October 2018

Independent of the initial cause of kidney disease, microvascular injury to the peritubular capillary network appears to play a central role in the development of interstitial fibrosis in both native and transplanted kidney disease. This association is explained by mechanisms such as the upregulation of profibrotic genes and epigenetic changes induced by hypoxia, capillary leakage, endothelial and pericyte transition to interstitial fibroblasts, as well as modifications in the secretome of endothelial cells. Alloimmune injury due to antibody-mediated rejection and ischemia-reperfusion injury are the two main etiologies of microvascular damage in kidney transplant recipients. The presence of circulating donor-specific anti-human leukocyte antigen (HLA) antibodies, histological findings, such as diffuse C4d staining in peritubular capillaries, and the extent and severity of peritubular capillaritis, are commonly used clinically to provide both diagnostic and prognostic information. Complement-dependent assays, circulating non-HLA antibodies, or evaluation of the microvasculature with novel imaging techniques are the subject of ongoing studies.
Plasma syndecan-1 in hemodialysis patients associates with survival and lower markers of volume status
Authors: Koch Josephine , Idzerda Nienke M. A. , Dam Wendy , Assa Solmaz , Franssen Casper F. M. , van den Born Jacob
Published: October 2018

Syndecan-1, a transmembrane heparan sulfate proteoglycan, associates with renal and cardiovascular functioning. We earlier reported syndecan-1 to be involved in renal tubular regeneration. We now examined plasma values of syndecan-1 in a hemodialysis cohort and its association with volume and inflammatory and endothelial markers in addition to outcome. Eighty-four prevalent hemodialysis patients were evaluated for their plasma syndecan-1 levels by ELISA before the start of hemodialysis, as well as 60, 180, and 240 min after start of dialysis. Patients were divided into sex-stratified tertiles based on predialysis plasma syndecan-1 levels. We studied the association between plasma levels of syndecan-1 and volume, inflammation, and endothelial markers and its association with cardiovascular events and all-cause mortality using Kaplan-Meier curves and Cox regression analyses with adjustments for gender, age, diabetes, and dialysis vintage. Predialysis syndecan-1 levels were twofold higher in men compared with women ( P = 0.0003). Patients in the highest predialysis plasma syndecan-1 tertile had a significantly higher ultrafiltration rate ( P = 0.034) and lower plasma values of BNP ( P = 0.019), pro-ANP ( P = 0.024), and endothelin ( P < 0.0001) compared with the two lower predialysis syndecan-1 tertiles. No significant associations with inflammatory markers were found. Cox regression analysis showed that patients in the highest syndecan-1 tertile had significantly less cardiovascular events and better survival compared with the lowest syndecan-1 tertile ( P = 0.02 and P = 0.005, respectively). In hemodialysis patients, higher plasma syndecan-1 levels were associated with lower concentrations of BNP, pro-ANP, and endothelin and with better patient survival. This may suggest that control of volume status in hemodialysis patients allows an adaptive tissue regenerative response as reflected by higher plasma syndecan-1 levels.
(Pro)renin receptor contributes to pregnancy-induced sodium-water retention in rats via activation of intrarenal RAAS and α-ENaC
Authors: Fu Ziwei , Hu Jiajia , Zhou Li , Chen Yanting , Deng Mokan , Liu Xiyang , Su Jiahui , Lu Aihua , Fu Xiaodong , Yang Tianxin
Published: October 2018

The (pro)renin receptor (PRR) is a new component of the renin-angiotensin-aldosterone system (RAAS) and regulates renin activity. The objective of the present study was to test potential roles of the renal PRR and intrarenal RAAS in the physiological status of late pregnancy. Late pregnant Sprague-Dawley rats were studied 19–21 days after sperm was observed in vaginal smears. Experiments were performed using age-matched virgin rats and late pregnant rats treated with the specific PRR inhibitor PRO20 (700 μg·kg−1·day−1sc for 14 days, 3 times/day for every 8 h) or vehicle. The indices of RAAS, including PRR, renin, angiotensin II, and aldosterone levels, were examined by immunoblotting, qRT-PCR, or ELISA. Further analyses of renal epithelial sodium channel (ENaC) expression, sodium-water retention, and plasma volume were performed. We first present evidence for the activation of intrarenal RAAS in late pregnant rats, including increases in urinary renin activity, active and total renin content, and prorenin content, angiotensin II and aldosterone excretion, in parallel with increased renal PRR expression and urinary soluble PRR excretion. Functional evidence demonstrated that PRR antagonism with PRO20 effectively suppressed the indices of intrarenal RAAS in late pregnant rats. In addition, our results revealed that renal α-ENaC expression, sodium-water retention, and plasma volume were elevated during late pregnancy, which were all attenuated by PRO20. In summary, the present study examined the renal mechanism of sodium-water retention and plasma volume expansion in late pregnant rats and identified a novel role of PRR in regulation of intrarenal RAAS and α-ENaC and thus sodium and fluid retention associated with pregnancy.
Continuously updating one’s predictions underlies successful interception
Authors: Brenner Eli , Smeets Jeroen B. J.
Published: October 2018

This paper reviews our understanding of the interception of moving objects. Interception is a demanding task that requires both spatial and temporal precision. The required precision must be achieved on the basis of imprecise and sometimes biased sensory information. We argue that people make precise interceptive movements by continuously adjusting their movements. Initial estimates of how the movement should progress can be quite inaccurate. As the movement evolves, the estimate of how the rest of the movement should progress gradually becomes more reliable as prediction is replaced by sensory information about the progress of the movement. The improvement is particularly important when things do not progress as anticipated. Constantly adjusting one’s estimate of how the movement should progress combines the opportunity to move in a way that one anticipates will best meet the task demands with correcting for any errors in such anticipation. The fact that the ongoing movement might have to be adjusted can be considered when determining how to move, and any systematic anticipation errors can be corrected on the basis of the outcome of earlier actions.
Three-dimensional tuning of head direction cells in rats
Authors: Shinder Michael E. , Taube Jeffrey S.
Published: October 2018

Head direction (HD) cells fire when the animal faces that cell’s preferred firing direction (PFD) in the horizontal plane. The PFD response when the animal is oriented outside the earth-horizontal plane could result from cells representing direction in the plane of locomotion or as a three-dimensional (3D), global-referenced direction anchored to gravity. To investigate these possibilities, anterodorsal thalamic HD cells were recorded from restrained rats while they were passively positioned in various 3D orientations. Cell responses were unaffected by pitch or roll up to ~90° from the horizontal plane. Firing was disrupted once the animal was oriented >90° away from the horizontal plane and during inversion. When rolling the animal around the earth-vertical axis, cells were active when the animal’s ventral surface faced the cell’s PFD. However, with the rat rolled 90° in an ear-down orientation, pitching the rat and rotating it around the vertical axis did not produce directionally tuned responses. Complex movements involving combinations of yaw-roll, but usually not yaw-pitch, resulted in reduced directional tuning even at the final upright orientation when the rat had full visual view of its environment and was pointing in the cell’s PFD. Directional firing was restored when the rat’s head was moved back-and-forth. There was limited evidence indicating that cells contained conjunctive firing with pitch or roll positions. These findings suggest that the brain’s representation of directional heading is derived primarily from horizontal canal information and that the HD signal is a 3D gravity-referenced signal anchored to a direction in the horizontal plane.

NEW & NOTEWORTHY This study monitored head direction cell responses from rats in three dimensions using a series of manipulations that involved yaw, pitch, roll, or a combination of these rotations. Results showed that head direction responses are consistent with the use of two reference frames simultaneously: one defined by the surrounding environment using primarily visual landmarks and a second defined by the earth’s gravity vector.
Stroke increases ischemia-related decreases in motor unit discharge rates
Authors: Murphy Spencer A. , Negro Francesco , Farina Dario , Onushko Tanya , Durand Matthew , Hunter Sandra K. , Schmit Brian D. , Hyngstrom Allison
Published: October 2018

Following stroke, hyperexcitable sensory pathways, such as the group III/IV afferents that are sensitive to ischemia, may inhibit paretic motor neurons during exercise. We quantified the effects of whole leg ischemia on paretic vastus lateralis motor unit firing rates during submaximal isometric contractions. Ten chronic stroke survivors (>1 yr poststroke) and 10 controls participated. During conditions of whole leg occlusion, the discharge timings of motor units were identified from decomposition of high-density surface electromyography signals during repeated submaximal knee extensor contractions. Quadriceps resting twitch responses and near-infrared spectroscopy measurements of oxygen saturation as an indirect measure of blood flow were made. There was a greater decrease in paretic motor unit discharge rates during the occlusion compared with the controls (average decrease for stroke and controls, 12.3 ± 10.0% and 0.1 ± 12.4%, respectively; P < 0.001). The motor unit recruitment thresholds did not change with the occlusion (stroke: without occlusion, 11.68 ± 5.83%MVC vs. with occlusion, 11.11 ± 5.26%MVC; control: 11.87 ± 5.63 vs. 11.28 ± 5.29%MVC). Resting twitch amplitudes declined similarly for both groups in response to whole leg occlusion (stroke: 29.16 ± 6.88 vs. 25.75 ± 6.78 Nm; control: 38.80 ± 13.23 vs 30.14 ± 9.64 Nm). Controls had a greater exponential decline (lower time constant) in oxygen saturation compared with the stroke group (stroke time constant, 22.90 ± 10.26 min vs. control time constant, 5.46 ± 4.09 min; P < 0.001). Ischemia of the muscle resulted in greater neural inhibition of paretic motor units compared with controls and may contribute to deficient muscle activation poststroke.

NEW & NOTEWORTHY Hyperexcitable inhibitory sensory pathways sensitive to ischemia may play a role in deficient motor unit activation post stroke. Using high-density surface electromyography recordings to detect motor unit firing instances, we show that ischemia of the exercising muscle results in greater inhibition of paretic motor unit firing rates compared with controls. These findings are impactful to neurophysiologists and clinicians because they implicate a novel mechanism of force-generating impairment poststroke that likely exacerbates baseline weakness.
Sources of Vascular Nitric Oxide and Reactive Oxygen Species and Their Regulation
Authors: Tejero Jesús , Shiva Sruti , Gladwin Mark T.
Published: October 2018

Nitric oxide (NO) is a small free radical with critical signaling roles in physiology and pathophysiology. The generation of sufficient NO levels to regulate the resistance of the blood vessels and hence the maintenance of adequate blood flow is critical to the healthy performance of the vasculature. A novel paradigm indicates that classical NO synthesis by dedicated NO synthases is supplemented by nitrite reduction pathways under hypoxia. At the same time, reactive oxygen species (ROS), which include superoxide and hydrogen peroxide, are produced in the vascular system for signaling purposes, as effectors of the immune response, or as byproducts of cellular metabolism. NO and ROS can be generated by distinct enzymes or by the same enzyme through alternate reduction and oxidation processes. The latter oxidoreductase systems include NO synthases, molybdopterin enzymes, and hemoglobins, which can form superoxide by reduction of molecular oxygen or NO by reduction of inorganic nitrite. Enzymatic uncoupling, changes in oxygen tension, and the concentration of coenzymes and reductants can modulate the NO/ROS production from these oxidoreductases and determine the redox balance in health and disease. The dysregulation of the mechanisms involved in the generation of NO and ROS is an important cause of cardiovascular disease and target for therapy. In this review we will present the biology of NO and ROS in the cardiovascular system, with special emphasis on their routes of formation and regulation, as well as the therapeutic challenges and opportunities for the management of NO and ROS in cardiovascular disease.
Antichronic Gastric Ulcer Effect of Zinc-Baicalin Complex on the Acetic Acid-Induced Chronic Gastric Ulcer Rat Model
Authors: Yang Hui , Lu Yi , Zeng Xiao-Feng , Li Ling , Zhang Rong-Ping , Ren Zhong-Kun , Liu Xu
Published: October 2018

Background. Baicalin (BA) has been shown to have anti-inflammatory and antioxidant activity. Zinc is a nutrient element. Objective. This study is aimed at investigating the antichronic gastric ulcer activity of Zn-Baicalin complex (BA-Zn) and its related mechanisms in an acetic acid-induced gastric ulcer rat model. Results. The severely ulcerated gastric mucosa of model rats had lower GSH-Px (52.21 ± 7.13) and SOD (7.03 ± 0.10) activity, and higher MDA (2.39 ± 0.03) content compared to sham rats. BA-Zn reduced the gastric ulcer index in a dose-dependent manner, significantly increased SOD activity and GSH-Px level, and reduced the MDA content and IL-8 and TNF-α levels in the gastric mucosa. BA-Zn (6.5 and 13 mg/kg) exerted a greater antiulcerogenic effect than both BA and zinc-gluconate, leading to a reduced ulcer index (18.43 ± 1.11, 15.00 ± 1.44), decreased MDA content (1.33 ± 0.07, 0.63 ± 0.01), and increased SOD activity (17.62 ± 0.11, 20.12 ± 0.32) and GSH-Px levels (102.12 ± 9.11, 120.25 ± 9.07). In addition, our results from Western blot suggested that BA-Zn (6.5 and 13 mg/kg) has a greater antiulcerogenic effect than both BA and zinc-gluconate. Conclusion. The BA-Zn complex possesses greater antichronic gastric ulcer properties compared to BA and zinc-gluconate due to its ability of oxidation resistance and anti-inflammatory effects.
Effects of Resistance Training on Immunoinflammatory Response, TNF-Alpha Gene Expression, and Body Composition in Elderly Women
Authors: Macêdo Santiago Luís Ângelo , Neto Lídio Gonçalves Lima , Borges Pereira Guilherme , Leite Richard Diego , Mostarda Cristiano Texeira , de Oliveira Brito Monzani Janaina , Sousa Wandson Rodrigues , Rodrigues Pinheiro Aruanã Joaquim Matheus , Navarro Francisco
Published: October 2018

The aim of this study was to determine the effects of resistance training on the immunologic response, body composition, tumor necrosis factor-alpha (TNF-alpha) gene expression obtained from blood leukocytes, and the cytokines interleukin-6, TNF-alpha, and C-reactive protein (CRP), in the elderly women (mean age 63 ± 2 y). A randomized controlled trial was performed using a bi-set training method for eight weeks in nineteen elderly women. Peripheral blood samples were collected by puncture in pretraining (Pre) and posttraining (Post) moments. In the resistance training group, there was a statistically significant decrease from 38.43 ± 9.48 pg/mL to 11.76 ± 5.19 pg/mL (p=0.01) in the serum levels of interleukin-6. Considering serum levels of TNF-alpha, there was a statistically significant difference, comparing the resistance training group at Pre (66.27 ± 10.31 pg/mL) and Post (37.85 ± 9.05 pg/mL) moments (p=0.01). In molecular analysis of TNF-alpha gene expression, there was a statistically significant decrease (p=0.007) between Pre (0.010 ± 0.01 ng/ml) and Post (0.0002 ± 0.0001 ng/ml) moments. Among CRP data, in the resistance training group, there was a statistically significant reduction, between Pre (2.04 ± 0.32 mg/L) and Post (0.90 ± 0.22 mg/L) moments (p=0.001). In the Control group, there was no statistical significance between these two moments. Therefore, the resistance training demonstrated changes in the TNF-alpha gene expression in elderly women, as well as decreased serum levels of interleukin-6, TNF-alpha, and CRP. Such conditions may be related to immune modulation and anti-inflammatory effects, since resistance training releases cytokines, especially interleukin-6, which acts as a TNF-alpha antagonist during exercise.
Ultra-Short-Term Multistep Prediction of Wind Power Based on Representative Unit Method
Authors: Yang Mao , Liu Lei , Cui Yang , Su Xin
Published: October 2018

With the continuous expansion of wind power grid scale, wind power prediction is an important means to reduce the adverse impact of large-scale grid integration on power grid: the higher prediction accuracy, the better safety, and economy of grid operation. The existing research shows that the quality of input sample data directly affects the accuracy of wind power prediction. By the analysis of measured power data in wind farms, this paper proposes an ultra-short-term multistep prediction model of wind power based on representative unit method, which can fully excavate data information and select reasonable data samples. It uses the similarity measure of time series in data mining, spectral clustering, and correlation coefficient to select the representative units. The least squares support vector machine (LSSVM) model is used as a prediction model for outputs of the representative units. The power of the whole wind farm is obtained by statistical upscaling method. And the number of representative units has a certain impact on prediction accuracy. The case study shows that this method can effectively improve the prediction accuracy, and it can be used as pretreatment method of data. It has a wide range of adaptability.
Chimeric RNA in Cancer and Stem Cell Differentiation
Authors: Elfman Justin , Li Hui
Published: October 2018

Gene fusions are considered hallmarks of cancer which can be produced by chromosomal rearrangements. These DNA-level fusion events may result in the expression of chimeric RNAs; however, chimeric RNAs can be also produced by intergenic splicing events. Chimeric transcripts created by the latter mechanism are regulated at the transcriptional level and thus present additional modes of action and regulation. They have demonstrated importance in normal cell physiology, and their dysregulation can induce oncogenesis and impact cell differentiation. In this review, we outline proven mechanisms through which intergenically spliced chimeric RNAs are involved in carcinogenesis. We highlight their similarity to canonical chimeric RNAs resulting from gene fusions as well as their unique qualities. Additionally, we review known roles of chimeric RNA in cell differentiation and propose means through which chimeric RNAs may be valuable as stage-specific markers or as targets for expression profiling.
The Effects of Platelet-Derived Growth Factor-BB on Bone Marrow Stromal Cell-Mediated Vascularized Bone Regeneration
Authors: Zhang Maolin , Yu Wenwen , Niibe Kunimichi , Zhang Wenjie , Egusa Hiroshi , Tang Tingting , Jiang Xinquan
Published: October 2018

Regenerative medicine for bone tissue mainly depends on efficient recruitment of endogenous or transplanted stem cells to guide bone regeneration. Platelet-derived growth factor (PDGF) is a functional factor that has been widely used in tissue regeneration and repair. However, the short half-life of PDGF limits its efficacy, and the mechanism by which PDGF regulates stem cell-based bone regeneration still needs to be elucidated. In this study, we established genetically modified PDGF-B-overexpressing bone marrow stromal cells (BMSCs) using a lentiviral vector and then explored the mechanism by which PDGF-BB regulates BMSC-based vascularized bone regeneration. Our results demonstrated that PDGF-BB increased osteogenic differentiation but inhibited adipogenic differentiation of BMSCs via the extracellular signal-related kinase 1/2 (ERK1/2) signaling pathway. In addition, secreted PDGF-BB significantly enhanced human umbilical vein endothelial cell (HUVEC) migration and angiogenesis via the phosphatidylinositol 3 kinase (PI3K)/AKT and ERK1/2 signaling pathways. We evaluated the effect of PDGF-B-modified BMSCs on bone regeneration using a critical-sized rat calvarial defect model. Radiography, micro-CT, and histological analyses revealed that PDGF-BB overexpression improved BMSC-mediated angiogenesis and osteogenesis during bone regeneration. These results suggest that PDGF-BB facilitates BMSC-based bone regeneration by enhancing the osteogenic and angiogenic abilities of BMSCs.
Investigation on Potential-Induced Degradation in a 50 MWp Crystalline Silicon Photovoltaic Power Plant
Authors: Huang Jingsheng , Li Hongtao , Sun Yaojie , Wang He , Yang Hong
Published: October 2018

The regular performance deterioration of P-type crystalline silicon solar modules and module strings caused by potential-induced degradation in a photovoltaic power plant was found in the field. The PID-affected solar modules dismounted from the photovoltaic power plant were further investigated systematically in the laboratory. For the first time, we found that the neutral point of voltage in a module string moved forward to the positive pole for a PID-affected module string as time goes on. Even if low positive voltage is applied to a PID-prone module, it could cause PID. The thermographic and electroluminescence (EL) images of a PID-affected module string also exhibit a regular degradation pattern. This is in good agreement with the measured power loss of the dismounted solar modules under standard test conditions. The results obtained in this paper show that the maximum power degradation rate of solar modules was as high as 53.26% after only one year of operation because of PID in the field. Due to the vast amount of solar modules and incomplete recovery, this is a terrible catastrophe for the owner of a power plant and module producer.
Genome Analysis of Rhodococcus Sp. DSSKP-R-001: A Highly Effective β-Estradiol-Degrading Bacterium
Authors: Zhao Hongyan , Tian Kejian , Qiu Qing , Wang Yu , Zhang Hongyan , Ma Shuang , Jin Shenbao , Huo Hongliang
Published: October 2018

We screened bacteria that use E2 as its sole source of carbon and energy for growth and identified them as Rhodococcus, and we named them DSSKP-R-001. For a better understanding of the metabolic potential of the strain, whole genome sequencing of Rhodococcus DSSKP-R-001 and annotation of the functional genes were performed. The genomic sketches included a predicted protein-coding gene of approximately 5.4 Mbp with G + C content of 68.72% and 5180. The genome of Rhodococcus strain DSSKP-R-001 consists of three replicons: one chromosome and two plasmids of 5.2, 0.09, and 0.09, respectively. The results showed that there were ten steroid-degrading enzymes distributed in the whole genome of the strain. The existence and expression of estradiol-degrading enzymes were verified by PCR and RTPCR. Finally, comparative genomics was used to compare multiple strains of Rhodococcus. It was found that Rhodococcus DSSKP-R-001 had the highest similarity to Rhodococcus sp. P14 and there were 2070 core genes shared with Rhodococcus sp. P14, Rhodococcus jostii RHA1, Rhodococcus opacus B4, and Rhodococcus equi 103S, showing evolutionary homology. In summary, this study provides a comprehensive understanding of the role of Rhodococcus DSSKP-R-001 in estradiol-efficient degradation of these assays for Rhodococcus. DSSKP-R-001 in bioremediation and evolution within Rhodococcus has important meaning.
Pixel-Label-Based Segmentation of Cross-Sectional Brain MRI Using Simplified SegNet Architecture-Based CNN
Authors: Khagi Bijen , Kwon Goo-Rak
Published: October 2018

Using deep neural networks for segmenting an MRI image of heterogeneously distributed pixels into a specific class assigning a label to each pixel is the concept of the proposed approach. This approach facilitates the application of the segmentation process on a preprocessed MRI image, with a trained network to be utilized for other test images. As labels are considered expensive assets in supervised training, fewer training images and training labels are used to obtain optimal accuracy. To validate the performance of the proposed approach, an experiment is conducted on other test images (available in the same database) that are not part of the training; the obtained result is of good visual quality in terms of segmentation and quite similar to the ground truth image. The average computed Dice similarity index for the test images is approximately 0.8, whereas the Jaccard similarity measure is approximately 0.6, which is better compared to other methods. This implies that the proposed method can be used to obtain reference images almost similar to the segmented ground truth images.
Case Report: Seaweed Bezoar Masquerading as a Malignant Obstruction
Authors: Abboud E. C. , Babic B.
Published: October 2018

Bezoars represent a rare cause of small bowel obstruction (SBO). Nonoperative management of bezoars includes use of endoscopy with mechanical or chemical dissolution methods. When obstruction persists, surgical intervention becomes necessary. Here, we present the case of an Asian woman with a SBO secondary to a phytobezoar masquerading as a malignancy. She presented with two days of acute-on-chronic abdominal pain that started after eating seaweed. Initial computed tomography (CT) scan showed a SBO with a jejunal transition point and ill-defined liver lesions, worrisome for a malignant obstruction with liver metastases. Further imaging, however, showed the resolution of these artifacts. Subsequent laparotomy revealed a small bowel loop with copious obstructing seaweed. A distal stricture was palpated, and the involved segment was resected. Intraoperative liver ultrasound was negative, and final pathology revealed benign small intestine with a mild stricture. Given the rarity of bezoar-related obstructions, the diagnosis is often delayed particularly when confounding factors exist such as our patient’s concomitant hepatic findings. Contrast-enhanced CT has a high sensitivity but a lower specificity in identifying bezoars. A high index of suspicion is therefore necessary especially when managing higher risk patients.
IgG4-Related Disease, the Malignancy Mimicker: Case Series from Bahrain
Authors: Haider Majeed , Haji Fatima , Alalwan Osama , Aljufairi Eman , Shah Tejal S.
Published: October 2018

IgG4-related disease is an evolving immune-mediated condition. The hallmark of this condition is IgG4(+) plasma cells infiltration of the affected organs accompanied by a variable degree of fibrosis and occasionally elevated serum IgG4 level. It links many conditions that were once recognized as isolated unrelated idiopathic single organ disorders (e.g., autoimmune pancreatitis, Mikulicz syndrome, and retroperitoneal fibrosis) under one umbrella. It usually presents clinically as tumor-like swelling of the involved organs that can be misdiagnosed as neoplasia. In this case series, we present four cases that were considered as neoplasia but turned out to be IgG4-related disease, we demonstrate the protean manifestations of this condition and variable organs involvement, and we share our experience in using rituximab as the steroid sparing immunosuppressant agent to control this disease.
Stress Management Training (SMT) Improves Coping of Tremor-Boosting Psychosocial Stressors and Depression in Patients with Parkinson’s Disease: A Controlled Prospective Study
Authors: Buhmann C. , Jungnickel D. , Lehmann E.
Published: October 2018

Background. Stress reduction and relaxation exercises are therapeutically suggested to patients with Parkinson’s disease (PD) and tremor, but data regarding efficacy or preferential methods are missing.Objective. To investigate the effect of a standardized stress management training (SMT) according to Kaluza on coping with tremor-boosting psychosocial stress factors.Methods. 8-week SMT was applied to 82 PD patients with tremor and 30 controls. Changes in stress-associated factors were measured applying four scales: Kaluza’s “warning signs for stress” and “stress-amplifying thoughts” and Beck Depression Inventory (BDI) and quality of life (PDQ-8). Short-term outcome (8 weeks) was evaluated in both groups, and long-term outcome (3–6 months) was evaluated only in PD patients.Results. At baseline, PDQ-8 was worse in PD patients compared to controls. PD patients improved significantly regarding short- and long-term outcome scores of “warning signs for stress,” “stress-amplifying thoughts,” and BDI scores, independently of disease severity or duration. Younger and male PD patients showed the best benefit. Controls improved comparably to PD patients but significantly only with respect to “stress-amplifying thoughts.” Retrospectively, 88% (29/33) of PD patients were rated SMT as helpful 12–18 months later. Self-practicing SMT exercises correlated significantly with subjectively better coping with tremor-related daily impairment and subjective short-term and long-term tremor reduction.Conclusion. SMT should be a part of therapy of PD patients with tremor.
Intravenous Anesthetic Protects Hepatocyte from Reactive Oxygen Species‐Induced Cellular Apoptosis during Liver Transplantation In Vivo
Authors: Yao Weifeng , Han Xue , Zhang Yihan , Guan Jianqiang , Ge Mian , Chen Chaojin , Wu Shan , Chen Jiaxin , Luo Gangjian , Huang Pinjie , Hei Ziqing
Published: October 2018

Background. Liver transplantation leads to liver ischemia/reperfusion (I/R) injury, resulting in early graft dysfunction and failure. Exacerbations of oxidative stress and inflammatory response are key processes in the development of liver I/R injury. Intravenous anesthetic propofol potent effects on free radical scavenging and protects livers against I/R injury. However, the role and mechanism of propofol‐mediated hepatic protection in liver transplantation is poorly understood. The aim of this study was to evaluate the role of propofol postconditioning in the liver I/R injury after liver transplantation. Methods. Forty‐eight rats were randomly divided into six groups: rats receiving either sham operation or orthotopic autologous liver transplantation (OALT) in the absence or presence of propofol (high dose and low dose) postconditioning or intralipid control or VAS2870 (Nox2 special inhibitor). Eight hours after OALT or sham operation, parameters of organ injury, oxidative stress, inflammation, and NADPH‐associated proteins were assessed. Results. After OALT, severe liver pathological injury was observed that was associated with increases of serum AST and ALT, which were attenuated by propofol postconditioning. In addition, especially high dose of propofol postconditioning reduced TNF‐α, IL‐1β, IL‐6, TLR4, and NF‐κB inflammatory pathway, accompanied with decrease of neutrophil elastase activity, MPO activity, 8‐isoprotane, p47phox and gp91phox protein expressions, and increase of SOD activity. Inhibition of Nox2 by VAS2870 conferred similar protective effects in liver transplantation. Conclusion. Liver transplantation leads to severe inflammation and oxidative stress with NADPH oxidase activation. Propofol postconditioning reduces liver I/R injury after liver transplantation partly via inhibiting NADPH oxidase Nox2 and the subsequent inflammation and oxidative stress.
Enhancing TFEB‐Mediated Cellular Degradation Pathways by the mTORC1 Inhibitor Quercetin
Authors: Huang Yi , Chen Yan , Shaw Amanda Marie , Goldfine Howard , Tian Junqiang , Cai Jiyang
Published: October 2018

Signaling pathways mediated by the mechanistic target of rapamycin (mTOR) play key roles in aging and age‐related diseases. As a downstream protein of mTOR, transcription factor EB (TFEB) controls lysosome biogenesis and cellular trafficking, processes that are essential for the functions of phagocytic cells like the retinal pigment epithelium (RPE). In the current study, we show that a naturally occurring polyphenolic compound, quercetin, promoted TFEB nuclear translocation and enhanced its transcriptional activity in cultured RPE cells. Activated TFEB facilitated degradation of phagocytosed photoreceptor outer segments. Quercetin is a direct inhibitor of mTOR but did not influence the activity of Akt at the tested concentration range. Our data suggest that the dietary compound quercetin can have beneficial roles in neuronal tissues by improving the functions of the TFEB‐lysosome axis and enhancing the capacities of cellular degradation and self‐renewal.
Enhanced Regeneration and Hepatoprotective Effects of Interleukin 22 Fusion Protein on a Predamaged Liver Undergoing Partial Hepatectomy
Authors: Zhou Heng , Xie Guomin , Mao Yudi , Zhou Ke , Ren Ruixue , Zhao Qihong , Wang Hua , Yin Shi
Published: October 2018

Liver ischemia-reperfusion injury (IRI) and regeneration deficiency are two major challenges for surgery patients with chronic liver disease. As a survival factor for hepatocytes, interleukin 22 (IL-22) plays an important role in hepatoprotection and the promotion of regeneration after hepatectomy. In this study, we aim to investigate the roles of an interleukin 22 fusion protein (IL-22-FP) in mice with a predamaged liver after a two-third partial hepatectomy (PHx). Predamaged livers in mice were induced by concanavalin A (ConA)/carbon tetrachloride (CCl4) following PHx with or without IL-22-FP treatment. A hepatic IRI mouse model was also used to determine the hepatoprotective effects of IL-22-FP. In the ConA/CCl4 model, IL-22-FP treatment alleviated liver injury and accelerated hepatocyte proliferation. Administration of IL-22-FP activated the hepatic signal transducer and activator of transcription 3 (STAT3) and upregulated the expression of many mitogenic proteins. IL-22-FP treatment prior to IRI effectively reduced liver damage through decreased aminotransferase and improved liver histology. In conclusion, IL-22-FP promotes liver regeneration in mice with predamaged livers following PHx and alleviates IRI-induced liver injury. Our study suggests that IL-22-FP may represent a promising therapeutic drug against regeneration deficiency and liver IRI in patients who have undergone PHx.
Synaptic Plasticity of Human Umbilical Cord Mesenchymal Stem Cell Differentiating into Neuron-like Cells In Vitro Induced by Edaravone
Authors: Shi Yunpeng , Nan Chengrui , Yan Zhongjie , Liu Liqiang , Zhou Jingjing , Zhao Zongmao , Li Depei
Published: October 2018

Objective. The human umbilical cord mesenchymal stem cells (hUMSCs) are characterized with the potential ability to differentiate to several types of cells. Edaravone has been demonstrated to prevent the hUMSCs from the oxidative damage, especially its ability in antioxidative stress. We hypothesized that Edaravone induces the hUMSCs into the neuron-like cells. Methods. The hUMSCs were obtained from the human umbilical cord tissue. The differentiation of hUMSCs was induced by Edaravone with three different doses: 0.65 mg/ml, 1.31 mg/ml, and 2.62 mg/ml. Flow cytometry was used to detect the cell markers. Protein and mRNA levels of nestin, neuron-specific enolase (NSE), and glial fibrillary acidic protein (GFAP) were detected by Western blot and RT-PCR. The expression of synaptophysin (SYN), growth-associated protein 43 (GAP43), and postsynaptic density 95 (PSD95) was detected by Real-Time PCR. Results. As long as the prolongation of the culture, the hUMSCs displayed with the long strips or long fusiform to fat and then characterized with the radial helix growth. By using flow cytometry, the cultured hUMSCs at the 3rd, 5th, and 10th passages were expressed with CD73, CD90, and CD105 but not CD11b, CD19, CD34, CD45, and HLA-DR. Most of the hUMSCs cultured with Edaravone exhibited typical nerve-immediately characters including the cell body contraction, increased refraction, and protruding one or more elongated protrusions, which were not found in the control group without addition of Edaravone. NSE, nestin, and GFAP were positive in these neuron-like cells. Edaravone dose-dependently increased expression levels of NSE, nestin, and GFAP. After replacement of maintenance fluid, neuron-like cells continued to be cultured for five days. These neuron-like cells were positive for SYN, PSD95, and GAP43. Conclusion. Edaravone can dose-dependently induce hUMSCs to differentiate into neuron-like cells that expressed the neuronal markers including NSE, nestin, and GFAP and synaptic makers such as SYN, PSD95, and GAP43.