bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of acute sleep deprivation on dynamic functional connectivity states
Authors: Li Changhong , Fronczek‐Poncelet Judith , Lange Denise , Hennecke Eva , Kroll Tina , Matusch Andreas , Aeschbach Daniel , Bauer Andreas , Elmenhorst Eva‐Maria , Elmenhorst David
Published: November 2019

Sleep deprivation (SD) could amplify the temporal fluctuation of spontaneous brain activities that reflect different arousal levels using a dynamic functional connectivity (dFC) approach. Therefore, we intended to evaluate the test–retest reliability of dFC characteristics during rested wakefulness (RW), and to explore how the properties of these dynamic connectivity states were affected by extended durations of acute sleep loss (28/52 hr). We acquired resting‐state fMRI and neuropsychological datasets in two independent studies: (a) twice during RW and once after 28 hr of SD (n = 15) and (b) after 52 hr of SD and after 14 hr of recovery sleep (RS; n = 14). Sliding‐window correlations approach was applied to estimate their covariance matrices and corresponding three connectivity states were generated. The test–retest reliability of dFC properties demonstrated mean dwell time and fraction of connectivity states were reliable. After SD, the mean dwell time of a specific state, featured by strong subcortical–cortical anticorrelations, was significantly increased. Conversely, another globally hypoconnected state was significantly decreased. Subjective sleepiness and objective performances were separately positive and negative correlated with the increased and decreased state. Two brain connectivity states and their alterations might be sufficiently sensitive to reflect changes in the dynamics of brain mental activities after sleep loss.
Safety and efficacy of transoral robotic and endoscopic thyroidectomy: The first 100 cases
Authors: Tae Kyung , Ji Yong Bae , Song Chang Myeon , Park Jeong Seon , Park Jung Hwan , Kim Dong Sun
Published: November 2019

Background

The aim of this study was to evaluate the safety and efficacy of transoral robotic and endoscopic thyroidectomy.

Methods

We analyzed and compared the first 100 cases of transoral robotic (71 cases) and endoscopic (29 cases) thyroidectomy with 207 cases of conventional transcervical thyroidectomy.

Results

Transoral thyroidectomy was completed successfully in all patients, except for three who were converted to the robotic facelift or transcervical approach. The mean operative time of the transoral procedure was significantly longer than that of the conventional procedure. Perioperative complications such as hypoparathyroidism, vocal cord palsy, hematoma, and seroma did not differ between the two groups. However, there were some unusual complications such as CO2 embolism, surgical site infection, skin trauma, burn, and ecchymosis in transoral thyroidectomy. Postoperative cosmesis was significantly better in the transoral group.

Conclusion

Transoral robotic and endoscopic thyroidectomy is feasible and comparable to conventional transcervical thyroidectomy in highly selected patients.
Going beyond health efficiency: What really matters?
Authors: Radojicic Milan , Jeremic Veljko , Savic Gordana
Published: November 2019

Both citizens and policymakers demand the best possible results from a country's healthcare system. It is of utmost importance to accurately and objectively assess the efficiency of a healthcare system and to note the key indicators, where resources are lost, and possibilities for improvement. This paper evaluates the efficiency of health systems in 38 countries, mainly members of the Organization for Economic Co‐operation and Development, using data envelopment analysis (DEA). In the first stage, bootstrapped Ivanovic distance is used to generate weights for the indicators, thus taking into consideration different country's goals, but not to the extent of reducing the possibility of comparison. The analysis shows that human resources are the most important health system resource and countries should pay special attention to developing and employing competent medical workers. The reorganization of human resources and the funds allocated to them could also increase efficiency. The second stage examines environmental indicators to find the causes of inefficiency. No proof is found that any one basic health system funding model produces better health outcomes than the others. Obesity is identified as a major issue.
How do Co‐ and Non‐Residential Children Impact your Subjective Life Expectancy: An Empirical Study on CHARLS Data?
Authors: Wu Hong
Published: November 2019

Background

Existing studies conclude SLE predicts decision‐making in the future. This paper studied how contacts with children influence subjective life expectancy (SLE) of the mid‐age and elderly in China. We also investigated the moderation effect of living arrangement preference (LAP). A better understanding of impact factors that contribute to the mid‐age and elderly's thoughts about their lifetime is essential for the late‐career financial planning and health interventions.

Methods

Our study examines the relationship between co‐ and non‐residential children and SLE by using two waves of data from China Health and Retirement Longitudinal Study (CHARLS).

Results

Our findings suggest that contacts with children help older people construct positive SLE. However, with an increased number of non‐residential children, older people will become pessimistic about their SLE. When older people prefer living alone, it decreases the impact of the number of non‐residential children on SLE.

Conclusion

Our results encourage children to live with their parents and contact their parents from time to time. Interventions that change their ideas about living arrangement preference may actually be useful for mid‐age and elderly. The best living arrangement should take the living arrangement preference of older people into consideration and give them the best arrangement according to their preference.
Trade‐size clustering and informed trading in global markets
Authors: Chen Tao
Published: November 2019

Based on intraday data across 41 markets, this study examines whether informed traders exploit trade‐size clustering. Clustering trades are documented to predict price movements, to generate perpetual return impact, and to improve informational efficiency. Collectively, these findings suggest that the clustering strategy is leveraged by the informed to cover up their activities in global markets. In addition, the cross‐country analysis indicates that larger market capacity and better legal protection, as two predominant institutional features, are associated with a lower level of informed‐trade clustering. Finally, such negative interaction attenuates in countries with lot‐size regulations and at bellwether stocks.
Optical coherence tomography as a noninvasive 3D real time imaging tool for the rapid evaluation of phenotypic variations in insect embryonic development
Authors: Su Ya , Wei Liya , Tan Hao , Li Jing , Li Wenping , Fu Lei , Wang Tongxin , Kang Le , Yao X. Steve
Published: November 2019

Noninvasive visualization of embryos at different development stages is crucial for the understanding of the basic developmental biology. It is therefore desirable to have an imaging tool capable of rapidly evaluating the effects of gene manipulation or genome editing in developing embryos for the studies of gene functions and genetic engineering. Here, we propose and demonstrate a novel use of optical coherence tomography (OCT) to noninvasively exam the embryonic development of the migratory locusts in real time with 3‐dimensional (3D) view capability. In particular, we obtain the sufficiently high spatial resolution tomographic 2D and 3D images of live locust embryos throughout their development processes. We show that not only we are able to noninvasively observe all previously known forms of blastokinesis as an embryo develops, such as anatrepsis, katatrepsis, revolution, rotation and diapauses, and determine their precise occurring time or duration, but also discover an unreported rotation form we named “twist.” In addition, with the OCT images we determined the exact occurring time of diapauses of the locusts from Tibetan plateau for the first time. Finally, we demonstrate that OCT systems can be used to rapidly capture the development defects of genetically modified embryos in which certain genes essential for embryonic development were suppressed by RNA interference. Our work shows that OCT is an enabling imaging tool with sufficient spatial resolution for the rapid evaluation of embryonic variations of small animals.
A comparative study on solubility improvement of tetracycline and dexamethasone by poly(propylene imine) and polyamidoamine dendrimers: An insight into cytotoxicity and cell proliferation
Authors: Najafi Faezeh , Salami‐Kalajahi Mehdi , Roghani‐Mamaqani Hossein , Kahaie‐Khosrowshahi Amir
Published: November 2019

Many of new chemical discovered in pharmaceutical industry are hydrophobic compounds. Various techniques have been used to overcome solubility problems of hydrophobic drugs in aqueous media. In the meantime, dendrimers have been considered for sustainability, nanoscale size, high carry capacity, tunable terminal functional groups in terms of drug delivery and solubility. In this work, we have synthesized poly(propylene imine) (PPI) dendrimer up to fifth generation using reduction of nitrile groups after Michael addition and also, polyamidoamine (PAMAM) dendrimer up to fourth generation using Michael addition and amidation reactions. fourth and fifth generations of PPI dendrimer and fourth and third generations of PAMAM dendrimer in different concentrations were used to evaluate the solubility of two hydrophobic drugs (tetracycline and dexamethasone). Furthermore, cytotoxicity of dendrimers and dendrimers/drugs hybrids was studied. The results showed that with increasing concentrations and also the generation of dendrimers, the solubility of these two hydrophobic drugs was increased. Cytotoxicity study through MTT assay against Osteoblast‐like cell line (MG‐63 cells) showed that dendrimers were relatively cytotoxic where adding dexamethasone caused higher cytotoxicity. However, tetracycline showed no significant effect on cytotoxicity whereas prevented cell proliferation.
LncRNA TMPO‐AS1 serves as a ceRNA to promote osteosarcoma tumorigenesis by regulating miR‐199a‐5p/WNT7B axis
Authors: Cui Huaan , Zhao Jiang
Published: November 2019

Osteosarcoma (OS) is a common kind of aggressive tumor in bone which was mostly identified in children and adolescents with extremely high risk of death. Accumulating research works have displayed that long noncoding RNAs (lncRNAs) exert an essential role in the development of multiple cancers. It has been reported that TMPO‐AS1 is an oncogene in cancers; nonetheless, its molecular mechanism in OS is totally unclear. Our present study elucidated that a remarkable overexpression of TMPO‐AS1 was found in OS tissues and cells. Moreover, TMPO‐AS1 depletion restrained Wnt/β‐catenin pathway and cell proliferation as well as facilitated cell apoptosis. Further molecular mechanism investigations showed that TMPO‐AS1 can sponge to miR‐199a‐5p. Moreover, miR‐199a‐5p was at a low level at OS cells. Importantly, miR‐199a‐5p's overexpression was associated with the OS cells' decreased proliferation and increased apoptosis. In addition, WNT7B was confirmed as a downstream gene of miR‐199a‐5p. Also the WNT7B expression was reversely modulated by miR‐199a‐5p and positively modulated by TMPO‐AS1. Rescue experiments suggested that downregulated WNT7B rescued miR‐199a‐5p inhibitor‐mediated repression on OS progression, but the treatment of LiCl counteracted the effect of WNT7B downregulation. In a word, TMPO‐AS1 serves as a competing endogenous RNA to boost osteosarcoma tumorigenesis by regulating miR‐199a‐5p/WNT7B axis, which provided an underlying therapeutic target for patients with OS.
CAPN2 acts as an indicator of hepatitis B virus to induce hepatic fibrosis
Authors: Feng Rui , Du Weixing , Lui Ping , Zhang Jun , Liu Yanqing
Published: November 2019

This study is aimed to investigate whether calpain 2 (CAPN2) serves as an indicator of the hepatitis B virus (HBV) to induce hepatic fibrosis. Differentially‐expressed genes (DEGs) in HBV‐induced hepatic fibrosis and normal liver tissues were analyzed, and signal pathway which was analyzed by the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis using DEGs. Next, the gene‐related network map was constructed using the Search Tool for the Retrieval of Interacting Genes. Moreover, CAPN2 protein expression, level of hepatic fibrosis, CAPN2 messenger RNA level, and protein levels of CAPN2, a‐SAM, COL3A1, COL1A1, and MAPK1 were determined using Immunohistochemistry (IHC), hematoxylin and eosin, RT‐qPCR, and western blot (WB), respectively. There were 420 DEGs screened in HBV‐induced hepatic fibrosis and normal liver tissues, among which, 373 were significantly upregulated and 47 were obviously downregulated. KEGG analysis showed that the upregulated DEGs were mainly concentrated in extracellular matrix‐receptor interaction, protein digestion, and absorption signaling pathways. The network diagram analysis showed that the DEGs, such as CAPN2, ITGAV, and CCR2, play the key role in the DEG network map, and CAPN2 related to hepatic fibrosis via MAPK1. The increased CAPN2 expression and obvious hepatic fibrosis was displayed in the HBV‐induced hepatic fibrosis tissues. In addition, HBV could induce CAPN2 expression, and the interference of CAPN2 could inhibit the expression of hepatic fibrosis markers, including a‐SAM, COL3A1, COL1A1, and MAPK1. CAPN2 is regarded as a biomarker of hepatic fibrosis induced by HBV.
Hepatitis B virus X protein upregulates alpha‐fetoprotein to promote hepatocellular carcinoma by targeting miR‐1236 and miR‐329
Authors: Zhang Chao , Liu Peng , Zhang Chuanbao
Published: November 2019

Hepatitis B virus (HBV) infection is the most common cause of hepatocellular carcinoma (HCC) worldwide, wherein the expression of alpha‐fetoprotein (AFP) is reactivated to promote tumorgenesis. Hepatitis B virus X protein (HBx) protein encoded by the HBV virus X gene has been considered to be oncogenic and implicated in hepatocarcinogenesis. However, the relationship between HBx and abnormal AFP expression in HCC is yet to be fully understood. To explore the potential regulation of HBx on AFP re‐expression in HCC, 97 HCC samples of different etiologies were analyzed, and extremely higher serum AFP levels were found in patients with HBsAg+. Analyses of HBV‐related HCC specimens showed that the expression of AFP was negatively correlated with the levels of miR‐1236 and miR‐329. Further analyses indicated that HBx promotes the expression of AFP by orchestrating the levels of miR‐1236 and miR‐329 both in vitro and in vivo. Specifically, miR‐1236 and miR‐329 bind to the potential target sequences in AFP mRNA 3′‐untranslated region to suppress its expression. HBx transfection resulted in the significant decrement of these microRNAs and increment of AFP expression. Moreover, AFP promotes the proliferation of hepatoma cells and attenuates the proapoptotic effect of chemotherapy agents. These findings revealed a novel regulatory mechanism of HBx on the abnormal AFP expression in HCC, which may provide a therapeutic approach for combating HBV‐related HCC by targeting the regulation of AFP expression.
Circular RNA circ_0074027 indicates a poor prognosis for NSCLC patients and modulates cell proliferation, apoptosis, and invasion via miR‐185‐3p mediated BRD4/MADD activation
Authors: Gao Ping , Wang Zhidong , Hu Zhanliang , Jiao Xuan , Yao Yue
Published: November 2019

Circular RNAs play an imperative role in cancer development and metastasis by regulating oncogenic and tumor‐suppressive pathways. However, the role and mechanism of circ_0074027 in non–small‐cell lung cancer (NSCLC) have not been elucidated. The expression levels of circ_0074027 were detected by qRT‐PCR. The link between circ_0074027 expression and clinicopathologic parameters was analyzed by Fisher's exact test. The prognostic role of circ_0074027 was investigated by Kaplan‐Meier and Cox regression analysis. Cell counting kit‐8 and flow cytometric assays were utilized to evaluate NSCLC cell proliferation and apoptosis, respectively. Wound scratch and Transwell tests were applied to detect cell migratory and invasive capacities. The interaction potential of circ_0074027 and miR‐185‐3p was analyzed by the circBank database, and verified by dual‐luciferase reporter assay. The downstream gene of miR‐185‐3p was also investigated. Circ_0074027 was elevated in NSCLC specimens and cell lines. Overexpressed circ_0074027 was related to more advanced TNM stages, poorer differentiation grade, and worse overall survival. Upregulated circ_0074027 increased the proliferation of H1299 cells by inhibiting cell apoptosis. Cell migration and invasion were enhanced after circ_0074027 overexpression. Silenced circ_0074027 caused the opposite effects in the A549 cell line. For mechanism investigation, circ_0074027 directly sponges miR‐185‐3p to enhance bromodomain‐containing protein 4 (BRD4) and MAPK‐activating death domain‐containing protein (MADD) expression levels at the posttranscriptional level. Furthermore, we found the oncogenic function of circ_0074027 is attributed to its modulation of BRD4 and MADD. Collectively, upregulated circ_0074027 in NSCLC accelerates cell progression via miR‐185‐3p/BRD4/MADD pathway as a competing endogenous RNA.
Mn(II) complex of a vitamin B6 Schiff base as an exclusive apoptosis inducer in human MCF7 and HepG2 cancer cells: Synthesis, characterization, and biological studies
Authors: Tabatabayi Zohreh S. , Homayouni‐Tabrizi Masoud , Neamati Ali , Beyramabadi S. Ali
Published: November 2019

Herein, a Mn(II) complex of the N,N′‐dipyridoxyl(1,4‐butanediamine) (═H2L) Schiff base has been newly synthesized. The synthesized complex was characterized by several experimental methods. In addition, the density functional theory approaches were used for theoretical identification of the complex. A good agreement between the computed and experimental infrared frequencies demonstrates validity of the optimized geometry for the synthesized complex. In a N2O2 manner, two azomethine nitrogens and two phenolate oxygens of the L2− ligand are coordinated to the Mn2+ metal ion. The biological studies indicate an efficient apoptotic and antioxidant activities of the synthesized [MnL(CH3OH)2] complex on both of the HepG2 and MCF7 cancer cells. Since it has been suggested that the complex is an exclusive potent antitumor for treatment of the human breast and liver cancers.
FBXO31 modulates activation of hepatic stellate cells and liver fibrogenesis by promoting ubiquitination of Smad7
Authors: He Huijuan , Dai Jialiang , Feng Jialing , He Qiang , Chen Xuling , Dai Wei , Xu Aizhong , Huang Haili
Published: November 2019

Liver fibrosis is a critical pathological process in the early stage of many liver diseases, including hepatic cirrhosis and liver cancer. However, the molecular mechanism is not fully revealed. In this study, we investigated the role of F‐box protein 31 (FBXO31) in liver fibrosis. We found FBXO31 upregulated in carbon tetrachloride (CCl4) induced liver fibrosis and in activated hepatic stellate cells, induced by transforming growth factor‐β (TGF‐β). The enforced expression of FBXO31 caused enhanced proliferation and increased expression of α‐smooth muscle actin (α‐SMA) and Col‐1 in HSC‐T6 cells. Conversely, suppression of FBXO31 resulted in inhibition of proliferation and decreased accumulation of α‐SMA and Col‐1 in HSC‐T6 cells. In addition, upregulation of FBXO31 in HSC‐T6 cells decreased accumulation of Smad7, the negative regulator of the TGF‐β/smad signaling pathway, and suppression of the FBXO31 increased accumulation of Smad7. Immunofluorescence staining showed FBXO31 colocalized with Smad7 in HSC‐T6 cells and in liver tissues of BALB/c mice treated with CCl4. Immunoprecipitation demonstrated FBXO31 interacted with Smad7. Moreover, FBXO31 enhanced ubiquitination of Smad7. In conclusion, FBXO31 modulates activation of HSCs and liver fibrogenesis by promoting ubiquitination of Smad7.
Pharmacokinetics of Para‐Aminosalicylic Acid and Its 2 Major Metabolites: A Potential Relationship to the Development of Gastrointestinal Intolerance
Authors: Adams Kim T. , Donald Peter R. , Abulfathi Ahmed A. , Diacon Andreas H. , Stander Marietjie A. , Reuter Helmuth
Published: November 2019

Para‐aminosalicylic acid (PAS), often the last drug remaining for treatment of drug‐resistant tuberculosis, is notorious for causing gastrointestinal intolerance; however, the cause of PAS intolerance is uncertain. The objective of this study was to assess relationships between peak concentrations of PAS administered as a granular slow‐release enteric coated formulation, and its metabolites acetyl‐PAS and glycine‐PAS, and intolerance. PAS and its metabolites were measured in 29 adult patients with drug‐resistant tuberculosis at Brooklyn Hospital, Cape Town, randomized to receive granular slow‐release enteric‐coated PAS 4 g twice daily or 8 g once daily for 1 week, followed by the alternative regimen. Concentrations of PAS and its metabolites were determined by liquid chromatography and tandem mass spectrometry, and a visual analogue scale evaluated intolerance. Spearman's correlation test assessed the relationship between maximum plasma concentrations (Cmax) and intolerance scores. A large interindividual variability was observed for the PAS Cmax (40.42‐68.55 mg/L) following 4 g twice daily; (62.69‐102.41 mg/L) for 8 g once daily and a similar wide Cmax range found for the metabolites acetyl‐PAS and glycine‐PAS. Twenty‐six patients reported at least 1 intolerance episode, but most visual analogue scale scores clustered around 0. Significant inverse associations were found between acetyl‐PAS Cmax and bloating (rho = –0.448; P = .025) and diarrhea (rho = –0.407; P = .044) for the twice‐daily regimen and a similar inverse association found for glycine‐PAS and diarrhea (rho = –0.412; P = .041). Plasma concentrations of the metabolites did not correlate with the occurrence of gastrointestinal symptoms, but higher metabolite concentrations correlated with lower intolerance scores; slow metabolism of PAS and its continued presence in the intestinal tract may be the main cause of intolerance.
Evaluation of gap formation at the composite resin‐tooth interface after using universal adhesives: In vitro SEM study using the replica technique
Authors: Kaczor‐Wiankowska Kinga , Lipa Sebastian , Krasowski Michał , Sokołowski Jerzy , Lewusz‐Butkiewicz Katarzyna , Nowicka Alicja
Published: November 2019

The aim of this study was to evaluate gap formation after using two universal adhesives, Peak Universal Bond (P), which contains chlorhexidine and Adhese Universal (A), which contains 10‐MDP monomer, and to compare them with two gold standard adhesives. The adhesives were tested in different etching modes, etch‐and‐rinse (ER) or self‐etch (SE), and under thermomechanical loading (TML). Two identical Class V cavities were prepared in each of 30 human third molar teeth, and resin‐composite restorations were made. Before and after TML, replicas of the restorations were prepared. Gap formation and their frequency according to the modified classification of Blunck and Zaslansky and the width of the maximum marginal gap (MG) were separately evaluated in enamel and dentin. Gap frequency did not differ significantly only in the enamel before TML, despite the use of different adhesives or etching modes. At both timepoints, the highest MG values were obtained with the Peak Universal Bond self‐etch (PSE) group in enamel (6.2 μm before TML, 12.2 μm after TML) and the Peak Universal Bond etch‐and‐rinse (PER) group in dentine (21.3 μm before TML, 35.5 μm after TML). After TML, there was a significant increase of gap frequency for Adhese universal self‐etch (ASE) group and MG values for PER, PSE, ASE groups at the resin‐enamel interface, and gap frequency and MG values for all groups at the resin‐dentin interface. Universal adhesive with 10‐MDP monomer have beneficial effect on the resin‐dentin interface, while chlorhexidine may reduce the resistance of the universal adhesive system to oral cavity conditions.
Implementing daily soft tissue image guidance with reduced margins for post‐prostatectomy radiotherapy: research‐based changes to clinical practice
Authors: Bell Linda J. , Eade Thomas , Hruby George , Bromley Regina , Kneebone Andrew
Published: November 2019

Introduction

We have previously demonstrated that daily soft tissue matching with reduced anisotropic margins provides an ideal balance between prostate bed coverage and meeting organ at risk constraints. The aim of this study was to evaluate the implementation of this approach in clinical practice.

Methods

Thirty‐eight radiation therapists (RTs) completed offline IGRT training involving six patients. After training was completed, this approach was implemented clinically. The first 24 patients were evaluated with a central review of match displacements and geographic miss (GM). An assessment of treatment times and planning parameters was also performed.

Results

During offline training, the anterior–posterior (AP) match discrepancy had the largest mean variation ranging from −0.46 to 0.06 cm and undetected geographic miss occurred in 17% of alignments. The mean time taken to treat the first 24 patients ranged from 12.2 to 20.6 min. The smaller anisotropic margin resulted in similar target coverage but achieved reduced doses to the bladder (V65Gy from 36% to 27%, V40Gy from 54% to 51%) and rectum (V65Gy from 20% to 19%, V60Gy from 27% to 24%, V40Gy from 42% to 38%). The matches of 806 CBCT images in 24 patients were reviewed. The mean match ranged from −0.12 to 0.17 cm AP, −0.14 to 0.14 cm superior–inferior (SI) and −0.04 to 0.04 cm left–right (LR). An undetected geographic miss was found in the prostate bed in 17 (2.1%) images and lymph nodes in 2 (0.2%) images.

Conclusions

Daily soft tissue IGRT with reduced anisotropic margins for post‐prostatectomy radiotherapy has been successfully implemented. RTs performed better with real‐time online matching than they did in offline training, perhaps influenced by having several RTs perform online matching. Daily soft tissue IGRT did not prolong treatment time.
Pathway‐based meta‐analysis for partially paired transcriptomics analysis
Authors: Fung Wing Tung , Wu Joseph T. , Chan Wai Man Mandy , Chan Henry H. , Pang Herbert
Published: November 2019

Pathway‐based differential expression analysis allows the incorporation of biological domain knowledge into transcriptomics analysis to enhance our understanding of disease mechanisms. To integrate information among multiple studies at the pathway level, pathway‐based meta‐analysis can be performed. Paired or partially paired samples are common in biomedical research. However, there are currently no existing pathway‐based meta‐analysis methods appropriate for paired or partially paired study designs.

In this study, we developed a pathway‐based meta‐analysis approach for paired or partially paired samples. Meta‐analysis on the transcriptomics profiles were conducted using p‐value‐based, rank‐based, and effect size‐based algorithms. The application of our approach was demonstrated using partially paired data from psoriasis transcriptomics studies.

Upon combining six transcriptomics studies, genes related to the cell cycle and DNA replication pathways are found to be highly perturbed in psoriatic lesional skin samples. Results were validated externally with independent RNA‐Seq data. Comparison with existing pathway meta‐analysis methods revealed consistent results, with our method showing higher detection power.

This study demonstrated the utility of our newly developed pathway‐based meta‐analysis that allows the incorporation of partially paired or paired samples. The proposed framework can be applied to omics data including but not limited to transcriptomics data.
A novel approach for identifying and addressing case‐mix heterogeneity in individual participant data meta‐analysis
Authors: Vo Tat‐Thang , Porcher Raphael , Chaimani Anna , Vansteelandt Stijn
Published: November 2019

Case‐mix heterogeneity across studies complicates meta‐analyses. As a result of this, treatments that are equally effective on patient subgroups may appear to have different effectiveness on patient populations with different case mix. It is therefore important that meta‐analyses be explicit for what patient population they describe the treatment effect. To achieve this, we develop a new approach for meta‐analysis of randomized clinical trials, which use individual patient data (IPD) from all trials to infer the treatment effect for the patient population in a given trial, based on direct standardization using either outcome regression (OCR) or inverse probability weighting (IPW). Accompanying random‐effect meta‐analysis models are developed. The new approach enables disentangling heterogeneity due to case mix from that due to beyond case‐mix reasons.
Long fallows allow soil regeneration in slash‐and‐burn agriculture
Authors: Lintemani Mariane Gonçalves , Loss Arcângelo , Mendes Camilo Sepulveda , Fantini Alfredo Celso
Published: November 2019

BACKGROUND

Slash‐and‐burn is a typical soil management system in tropical regions, in which the use of fire and the fallow time are key factors for controlling the dynamics of the physical and chemical attributes of the soil. The present study evaluated the ability of the fallow period to regenerate the soil, making it similar to the soil of a mature native forest, and compared it with other agricultural soils using a slash‐and‐burn chronosequence. Soil samples (0–5, 5–10 and 10–20 cm) were collected in areas with slash‐and‐burn agriculture [2‐year crop (cassava); 10 and 15‐years fallow] and in nearby areas with eucalyptus forest plantation, agroforestry system and mature native forest.

RESULTS

Slash‐and‐burn agriculture does not alter soil bulk density; however, it reduces aggregate geometric mean diameter (GMD). A 15‐year fallow can restore the GMD to values similar to those other areas. The sensitivity index of GMD shows the improvement of aggregation after a 15‐year fallow. Total organic carbon decreases in a 2‐year crop but increases in a 10‐year fallow. A 15‐year fallow increases particulate organic carbon and mineral‐associated organic carbon compared to a 2‐year crop. Total nitrogen, particulate nitrogen and mineral‐associated nitrogen decrease in the years following the burning but increase throughout a 15‐year fallow.

CONCLUSION

The results of the chemical and physical attributes evaluated indicate that a fallow period of 15 years or more after a crop cycle in slash‐and‐burn agriculture can restore the original soil conditions. The soil quality conservation in the slash‐and‐burn agriculture is superior to that of continued cultivation of agricultural crops, or monoculture plantations. © 2019 Society of Chemical Industry
Diverse food in urban gardens in the promotion of food and nutrition security in Brazil: a review
Authors: Sant'Anna de Medeiros Natália , do Carmo Davi Lopes , Priore Silvia Eloiza , Santos Ricardo Henrique Silva
Published: November 2019

Food and nutrition security can be supported by an urban garden. The present study comprises a critical reflection on the difficulty of producing food in urban gardens in Brazil and shows the potential of food production and the obstacles to its expansion. In addition, issues related to the agroecological management of gardens are addressed and suggestions are made to improve the proposed public policies. Urban gardens are multifunctional and have social, economic and environmental impacts. They are strategically important for supporting low‐income families and urban development. Through urban gardens, diverse foods and quality foods can be produced for self‐consumption. This review highlights the importance of generating detailed information on urban gardens in Brazil to support policies aimed at this sector. Long‐term and multidisciplinary studies are needed to evaluate the relationship between food production in urban gardens and household food and nutrition security. This approach revealed a lack of information on the amount of food produced by Brazilians in their gardens and consumed by the household. In addition, there is little information on the management of production. There is a gap relating to the impact of food produced in urban gardens and the prevalence of food and nutrition security. © 2019 Society of Chemical Industry
U.S. News and World Report hospital ranking and surgical outcomes among patients undergoing surgery for cancer
Authors: Mehta Rittal , Merath Katiuscha , Farooq Ayesha , Sahara Kota , Tsilimigras Diamantis I. , Ejaz Aslam , Hyer J. Madison , Paredes Anghela Z. , Dillhoff Mary , Cloyd Jordan M. , Pawlik Timothy M.
Published: November 2019

Background

Despite the popularity of the U.S. News and World Report (USNWR) hospital rankings among the general public, the relationship between hospital rankings and actual patient outcomes for major cancers remains poorly investigated.

Methods

Medicare Inpatient Standard Analytic Files were queried from 2013–2015 to assess the relationship of postoperative outcomes and Medicare expenditures among patients undergoing surgery for colorectal, lung, esophageal, pancreatic, and liver cancer at hospitals ranked in the top‐50 USNWR vs hospitals ranked below 50.

Results

Among 94 599 patients, 13 217 vs 81 382 patients underwent surgery at a top‐50 hospital versus a non‐top 50 ranked hospital. Other than among patients who underwent colorectal surgery, the odds of postoperative complications were lower at top ranked vs non‐top ranked hospitals (colorectal: OR, 1.46, 95% CI, 1.28‐1.65; lung: OR, 0.73, 95% CI, 0.61‐0.87; esophagus: OR, 0.70, 95% CI, 0.52‐0.94; pancreas: OR, 0.81, 95% CI, 0.70‐0.94; liver: OR, 0.85, 95% CI, 0.69‐1.04). Moreover, the odds of 90‐day mortality were lower at top ranked hospitals vs non‐top ranked hospitals (colorectal: OR, 0.59, 95% CI, 0.48‐74; lung: OR, 0.66, 95% CI, 0.53‐0.82; esophagus: OR, 0.56, 95% CI, 0.40‐0.80; pancreas: OR, 0.51, 95% CI, 0.40‐0.65; liver: OR, 0.61, 95% CI, 0.44‐0.84). Outcomes were comparable among hospitals within the top‐50 rank.

Conclusion

Mortality rates were lower at hospitals in the top‐50 USNWR versus non‐top ranked, yet hospitals within the top‐50 USNWR rankings had comparable outcomes.
Manganese/iron‐supported sulfate‐dependent anaerobic oxidation of methane by archaea in lake sediments
Authors: Su Guangyi , Zopfi Jakob , Yao Haoyi , Steinle Lea , Niemann Helge , Lehmann Moritz F.
Published: November 2019

Anaerobic oxidation of methane (AOM) by methanotrophic archaea is an important sink of this greenhouse gas in marine sediments. However, evidence for AOM in freshwater habitats is rare, and little is known about the pathways, electron acceptors, and microbes involved. Here, we show that AOM occurs in anoxic sediments of a sulfate‐rich lake in southern Switzerland (Lake Cadagno). Combined AOM‐rate and 16S rRNA gene‐sequencing data suggest that Candidatus Methanoperedens archaea are responsible for the observed methane oxidation. Members of the Methanoperedenaceae family were previously reported to conduct nitrate‐ or iron/manganese‐dependent AOM. However, we demonstrate for the first time that the methanotrophic archaea do not necessarily rely upon these oxidants as terminal electron acceptors directly, but mainly perform canonical sulfate‐dependent AOM, which under sulfate‐starved conditions can be supported by metal (Mn, Fe) oxides through oxidation of reduced sulfur species to sulfate. The correspondence of high abundances of Desulfobulbaceae and Candidatus Methanoperedens at the same sediment depth confirms the interdependence of anaerobic methane‐oxidizing archaea and sulfate‐reducing bacteria. The relatively high abundance and widespread distribution of Candidatus Methanoperedens in lake sediments highlight their potentially important role in mitigating methane emissions from terrestrial freshwater environments to the atmosphere, analogous to ANME‐1, ‐2, and ‐3 in marine settings.
In‐Plane Photonic Crystal Devices using Fano Resonances
Authors: Bekele Dagmawi , Yu Yi , Yvind Kresten , Mork Jesper
Published: November 2019

Nanocavity devices enabling concentration of light in a very small volume have resulted in several interesting applications over the past years. Of particular interest are the asymmetric resonance lineshapes known as Fano resonances, which result from the interference between a discrete mode of the nanocavity and a continuum of background modes. Compared to the conventional symmetric Lorentzian lineshape, asymmetric Fano lineshapes enable novel or improved device structures for use in optical switches, sensors, lasers, and narrow band filters. Herein, the use of Fano lineshapes in photonic crystal membranes for realizing various optical signal processing functionalities is reviewed. The basic theory of Fano resonances is presented, different photonic crystal Fano device geometries are discussed, the nonlinear processes empowering the devices are explained, and an overview of all‐optical signal processing demonstrations based on Fano resonances is given.
Normal Doppler Frequency Shift in Negative Refractive‐Index Systems
Authors: Lin Xiao , Zhang Baile
Published: November 2019

Besides the well‐known negative refraction, a negative refractive‐index material can exhibit another two hallmark features, which are the inverse Doppler effect and backward Cherenkov radiation. The former is known as the motion‐induced frequency shift that is contrary to the normal Doppler effect, and the latter refers to the Cherenkov radiation whose cone direction is opposite to the source's motion. Here these two features are combined and the Doppler effect inside the backward Cherenkov cone is discussed. It is revealed that the Doppler effect is not always inversed but can be normal in negative refractive‐index systems. A previously un‐reported phenomenon of normal Doppler frequency shift is proposed in a regime inside the backward Cherenkov cone, when the source's velocity is two times faster than the phase velocity of light. A realistic metal–insulator–metal structure, which supports metal plasmons with an effective negative refractive index, is adopted to demonstrate the potential realization of this phenomenon.
Arbitrary Energy‐Preserving Control of Optical Pulse Trains and Frequency Combs through Generalized Talbot Effects
Authors: Romero Cortés Luis , Maram Reza , Guillet de Chatellus Hugues , Azaña José
Published: November 2019

Trains of optical pulses and optical‐frequency combs are periodic waveforms with deep implications for a wide range of scientific disciplines and technological applications. Recently, phase‐only signal‐processing techniques based upon the theory of Talbot self‐imaging have been demonstrated as simple and practical means for user‐defined periodicity control of optical pulse trains and combs. The resulting schemes implement a desired repetition period control without introducing any noise or distortion, while ideally preserving the entire energy content of the signal. Here, recent developments on phase‐only signal‐processing schemes for periodicity control based on temporal and spectral self‐imaging are reviewed. As a central contribution, a comprehensive theory of generalized Talbot self‐imaging, so called phase‐controlled Talbot effect, is presented, comprising all the different approaches proposed to date. In particular, a closed unified mathematical framework for the design of the spectral and temporal phase manipulations that enable full arbitrary control of the period of repetitive signals is developed. The reported numerical studies fully validate the presented theoretical framework and shed light on crucial aspects of the proposed methods, consistently with previously reported experimental results. Important considerations concerning the practical, real‐world implementation of the described schemes, according to the needed specifications for different applications, are also discussed.
FUNCTIONAL METABOLOMICS DECIPHER BIOCHEMICAL FUNCTIONS AND ASSOCIATED MECHANISMS UNDERLIE SMALL‐MOLECULE METABOLISM
Authors: Hu Longlong , Liu Jingjing , Zhang Wenhua , Wang Tianyu , Zhang Ning , Lee Yie Hou , Lu Haitao
Published: November 2019

Metabolism is the collection of biochemical reactions enabled by chemically diverse metabolites, which facilitate different physiological processes to exchange substances and synthesize energy in diverse living organisms. Metabolomics has emerged as a cutting‐edge method to qualify and quantify the metabolites in different biological matrixes, and it has the extraordinary capacity to interrogate the biological significance that underlies metabolic modification and modulation. Liquid chromatography combined with mass spectrometry (LC/MS), as a robust platform for metabolomics analysis, has increased in popularity over the past 10 years due to its excellent sensitivity, throughput, and versatility. However, metabolomics investigation currently provides us with only phenotype data without revealing the biochemical functions and associated mechanisms. This limitation indeed weakens the core value of metabolomics data in a broad spectrum of the life sciences. In recent years, the scientific community has actively explored the functional features of metabolomics and translated this cutting‐edge approach to be used to solve key multifaceted questions, such as disease pathogenesis, the therapeutic discovery of drugs, nutritional issues, agricultural problems, environmental toxicology, and microbial evolution. Here, we are the first to briefly review the history and applicable progression of LC/MS‐based metabolomics, with an emphasis on the applications of metabolic phenotyping. Furthermore, we specifically highlight the next era of LC/MS‐based metabolomics to target functional metabolomes, through which we can answer phenotype‐related questions to elucidate biochemical functions and associated mechanisms implicated in dysregulated metabolism. Finally, we propose many strategies to enhance the research capacity of functional metabolomics by enabling the combination of contemporary omics technologies and cutting‐edge biochemical techniques. The main purpose of this review is to improve the understanding of LC/MS‐based metabolomics, extending beyond the conventional metabolic phenotype toward biochemical functions and associated mechanisms, to enhance research capability and to enlarge the applicable scope of functional metabolomics in small‐molecule metabolism in different living organisms.
Targeting the Microglial NLRP3 Inflammasome and Its Role in Parkinson's Disease
Authors: Haque Md. Ezazul , Akther Mahbuba , Jakaria Md. , Kim In‐Su , Azam Shofiul , Choi Dong‐Kug
Published: November 2019

Excessive activation of microglia and subsequent release of proinflammatory cytokines play a crucial role in neuroinflammation and neurodegeneration in Parkinson's disease (PD). Components of the nucleotide‐binding oligomerization domain and leucine‐rich‐repeat‐ and pyrin‐domain‐containing 3 inflammasome complex, leucine‐rich‐repeat‐ and pyrin‐domain‐containing 3, caspase‐1, and apoptosis‐associated speck‐like protein containing a CARD, are highly expressed in activated microglia in PD patient brains. Findings suggest that neurotoxins, aggregation of α‐synuclein, mitochondrial reactive oxygen species, and disrupted mitophagy are the key regulators of microglial leucine‐rich‐repeat‐ and pyrin‐domain‐containing 3 inflammasome activation and release of interleukin‐1β and interleukin‐18 caspase‐1‐mediated pyroptotic cell death in the substantia nigra of the brain. Although this evidence suggests the leucine‐rich‐repeat‐ and pyrin‐domain‐containing 3 inflammasome may be a potential drug target for treatment of PD, the exact mechanism of how the microglia sense these stimuli and initiate leucine‐rich‐repeat‐ and pyrin‐domain‐containing 3 inflammasome signaling is unknown. Here, the molecular mechanism and regulation of microglial leucine‐rich‐repeat‐ and pyrin‐domain‐containing 3 inflammasome activation and its role in the pathogenesis of PD are discussed. Moreover, the potential of both endogenous and synthetic leucine‐rich‐repeat‐ and pyrin‐domain‐containing 3 inflammasome modulators, long noncoding RNA, microRNA to develop novel therapeutics to treat PD is presented. Overall, we recommend that the microglial leucine‐rich‐repeat‐ and pyrin‐domain‐containing 3 inflammasome can be a potential target for PD treatment. © 2019 International Parkinson and Movement Disorder Society
Characterizing meteorological and hydrological droughts: A case study of the Gediz River Basin, Turkey
Authors: Kumanlioglu Ahmet Ali
Published: November 2019

The determination of the drought characteristics of a basin that feeds a reservoir and provides water for agricultural irrigation or energy production is important for the sustainable management of reservoirs. In the present study, the meteorological and hydrological droughts of the upper basins feeding the Demirköprü Reservoir in the Gediz River Basin of Turkey are examined over one, three, six and 12 month timescales. The methods used include the standardized precipitation index (SPI) and the standardized precipitation evapotranspiration index (SPEI) for defining meteorological droughts, and the standardized runoff index (SRI) method for defining hydrological droughts. The results show that the wet periods are dominant in the water years before 1984, and the dry periods occurred more frequently and were longer after this year in the basin. Owing to a temperature increase, it is determined that the effect of potential evapotranspiration losses on drought events has increased in the years after 2000, and the droughts that occurred after this year have happened more intensively in the basin. The results also show that both the meteorological and hydrological drought trends of the basin are prone to dry conditions and no that change is expected in these trends in the near future. Considering the predicted global climate changes, the results provide a source for describing the characteristics of the meteorological and hydrological droughts observed in the basins for the sustainable management of reservoirs which have a large irrigation area or energy production.
Design of a dual‐polarized reflect‐transmit‐array
Authors: Xi Baokun , Xue Qianzhong , Cai Yang , Wang Yong , Yang Shaopeng , Zhang Rui , Zhang Lianzheng
Published: November 2019

A new low‐profile, dual‐polarized reflect‐transmit‐array antenna which combines the linearly polarized reflectarray (RA) and circularly polarized transmitarray (TA) with a shared aperture is proposed. The antenna adopts a three‐parallel dipole and a two‐surface dipole connected by vias as radiating elements in RA and TA design, respectively. By using the polarized grid, TA is decoupled from RA, which greatly enhanced the efficiency and significantly simplified the whole design process. To minimize the overall thickness, the TA employs double metal layer with two vias instead of multilayer structures. The operating mechanism of the TA layer is then analyzed by characteristic mode analysis. An array prototype with a 256‐mm circular aperture was fabricated and experimentally verified. The measured gains in reflect mode and transmit mode is 27.5 dB with 54.3% aperture efficiency and 26.7 dB with 45.1% aperture efficiency, respectively. This prototype confirms the feasibility of designing a low‐profile, multifunctional, wideband, and high‐efficiency reflect‐transmit array.