bluuebunny/crossref_metadata_2025 huggingface dataset:
Combination of noninvasive methods in diagnosis of infertile women with minimal or mild endometriosis, a retrospective study in China
Authors: Yu Huaying , Li Baijia , Li TinChiu , Zhang Songying , Lin Xiaona
Published: August 2019

This study means to investigate a combination of noninvasive methods in diagnosis of minimal or mild endometriosis expecting to narrow down the range of laparoscopic exploration for female infertility.

It is a retrospective case control study of totally 447 patients suspected unexplained infertility before surgery were eligible from May 2012 to February 2017. Of these, 299 patients were laparoscopy-proved minimal or mild endometriosis group, the remaining 148 patients served as control group (normal pelvis). Preoperative age, duration of infertility, type of infertility, body mass index, baseline follicle-stimulating hormone, anti-Müllerian hormone, serum CA125, clinical symptoms, findings on vagino-recto-abdominal examinations and pregnancy prognosis had been recorded. Every variable and their combinations were evaluated.

Any single factor had limited diagnostic value. The cut-off value for CA125 was 19.25 IU/L. Parallel testing had a higher sensitivity at 81.3%. Serial tests of vagino-recto-abdominal examination combined with dysmenorrhea or positive CA125 got reasonable sensitivity (51.4% and 49%), remarkable high specificities (95.7% and100%) and Positive Predictive Value (96.4% and 100%). Multivariate logistic regression identified the following factors in decreasing order of importance: (1) vagino-recto-abdominal examinations, (2) CA125, (3) dysmenorrhea, their ORs being 16.148, 3.796, and 2.809, respectively. The spontaneous pregnancy rate (50.8%) in minimal or mild endometriosis was higher than control (35.6%, P = .043).

A combination of noninvasive diagnostic methods had certain preoperative diagnostic value of minimal or mild endometriosis, which might benefit some patients from avoiding laparoscopic surgery.
Serum metabolome and targeted bile acid profiling reveals potential novel biomarkers for drug-induced liver injury
Authors: Ma Zhenhua , Wang Xiaomei , Yin Peiyuan , Wu Ruihong , Zhou Lina , Xu Guowang , Niu Junqi
Published: August 2019

This study aims to determine the non-invasive, reliable and sensitive biochemical parameters for the diagnosis of drug-induced liver injury (DILI).

Ultra-high performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) and selected reaction monitoring (SRM) were used to profile the serum metabolome and quantify 15 targeted bile acid metabolites, respectively, in samples obtained from 38 DILI patients and 30 healthy controls.

A comparison of the resulting serum metabolome profiles of the study participants revealed significant differences between DILI patients and healthy controls. Specifically, serum palmitic acid, taurochenodeoxycholic acid, glycocholic acid (GCA), and tauroursodeoxycholic acid (TUDCA) levels were significantly higher, and serum lysophosphatidylethanolamine levels were significantly lower in DILI patients vs healthy controls (P < .001). Furthermore, the SRM assay of bile acids revealed that the increase in GCA, taurocholic acid (TCA), TUDCA, glycochenodeoxycholic acid (GCDCA), glycochenodeoxycholic sulfate (GCDCS), and taurodeoxycholic acid (TDCA) corresponded to a higher degree of liver damage. These results also indicate that serum concentrations of chenodeoxycholic acid (CDCA), deoxycholic acid (DCA) and lithocholic acid (LCA) were significantly lower in patients with severe DILI, when compared to healthy controls, and that this decrease was closely correlated to the severity of liver damage.

Taken together, these results demonstrate that bile acids could serve as potential biomarkers for the early diagnosis and severity of DILI.
Hyperglycemia is associated with poor in-hospital outcome in elderly patients with acute ischemic stroke
Authors: Zhao Lei , Wang Li , Lu Meihua , Hu Wei , Xiu Shuangling
Published: August 2019

Fasting hyperglycemia is associated with poor neurologic outcome in acute ischemic stroke (AIS), but its relationship with in-hospital outcome in elderly patients remains largely unknown. To assess the association of in-hospital outcome with fasting plasma glucose (FPG) levels at admission in individuals with AIS.

This retrospective propensity score-matched case–control study included patients aged over 60 years suffering from AIS and who were admitted to the emergency department from November 2013 to October 2016. Subjects were grouped into the poor-outcome and good-outcome groups based on mortality and intensive care unit (ICU) admission.

The poor- and good-outcome groups comprised 74 and 1927 cases, respectively, before propensity score matching (PSM), and 74 and 296 cases, respectively, after PSM. Univariable logistic regression analysis showed that initial FPG after admission was associated with poor in-hospital outcome. Multivariable logistic regression analysis showed that initial FPG after admission was an independent predictor of poor in-hospital outcome (odds ratio = 1.11, 95% confidence interval: 1.037–1.188, P = .003).

This study used PSM and strongly suggests that FPG is an independent predictive factor of poor in-hospital outcome in elderly patients with AIS. High initial FPG levels after admission may predict poor in-hospital outcome. Prospective studies are needed to confirm these findings.
The Use of Closing Questions in Qualitative Research
Authors: Sowicz Timothy Joseph , Sefcik Justine S. , Teng Helen L. , Irani Elliane , Kelly Terri-Ann , Bradway Christine
Published: August 2019

Background

Scarce and differing reasons for including closing questions in qualitative research exist, but how data generated from these questions are used remains uncertain.

Objectives

The purpose of the study was to understand if and how researchers use closing questions in qualitative research, specifically the research questions were: (a) “Why do qualitative researchers include or exclude closing questions during interviews?” and (b) “How do qualitative researchers use data from closing questions?”

Methods

A qualitative descriptive design using a single, asynchronous, web-based, investigator-designed survey containing 14 items was used to collect data. Convenience and snowball sampling were used to recruit participants. Data were analyzed using descriptive statistics and qualitative content analysis. Codes were developed from the qualitative data. Subcategories were derived from similar codes, and these subcategories were further scrutinized and were used to create broad categories.

Results

The number of respondents per question ranged from 76 to 99; most identified nursing and sociology as their academic disciplines, lived in the United States, and were involved in qualitative research for 1–10 years. Data, the interview, the interviewee, and the interviewer were broad categories to emerge as reasons for including closing questions. Only one respondent reported a reason for excluding closing questions. The uses of closing question data were described in four broad categories: analysis, data, the interview guide, and inquiry.

Discussion

Researchers frequently included closing questions in qualitative studies. The reasons for including these questions and how data are used vary, and support limited previously published literature. One unique reason, adding “new breath” to the interview, emerged. Study findings can aid qualitative researchers in deciding whether to include closing questions.
Napsin-A and AMACR are Superior to HNF-1β in Distinguishing Between Mesonephric Carcinomas and Clear Cell Carcinomas of the Gynecologic Tract
Authors: Pors Jennifer , Segura Sheila , Cheng Angela , Ji Jennifer X. , Tessier-Cloutier Basile , Cochrane Dawn , Fix Daniel J. , Park Kay , Gilks Blake , Hoang Lynn
Published: August 2019

Mesonephric carcinoma is a rare gynecologic neoplasm commonly mistaken for clear cell carcinoma, because of their overlapping morphologic features. Both tumors are negative for estrogen receptor and p16, magnifying this diagnostic dilemma. Recently, hepatocyte nuclear factor-1 beta (HNF-1β), a marker for clear cell carcinoma, has also been shown to be positive in mesonephric carcinomas. Other more recent markers for clear cell carcinoma, however, such as Napsin-A and alpha-methylacyl-CoA racemase (AMACR), have not yet been studied in mesonephric carcinomas. Here we examine HNF-1β, AMACR, and Napsin-A immunohistochemistry in 18 mesonephric and 55 endometrial/cervical clear cell carcinomas. HNF-1β was considered positive if nuclear staining was present in ≥70% of cells and at least moderate intensity; for Napsin-A and AMACR, any cytoplasmic staining was considered positive (≥1%). H-scores were determined by multiplying the intensity score by proportion score. HNF-1β was positive in a substantial portion of mesonephric carcinomas (9/18, 50%; H-score 98) and clear cell carcinomas (34/55, 62%; H-score 163) and did not distinguish between the 2 entities (specificity, 50%; P-value of H-score=0.08). Napsin-A and AMACR expression was significantly higher in clear cell [43/55 (78%) and 41/55 (75%), respectively] than mesonephric carcinomas [4/18 (22%) and 4/18 (22%) respectively], and helpful in this differential (specificity: 78% and 78%; P<0.05 for both). When Napsin-A and AMACR staining were seen in mesonephric carcinomas, staining was focal (≤5%), whereas staining in clear cell carcinomas was patchy/diffuse. In summary, Napsin-A and AMACR are helpful in distinguishing mesonephric carcinomas from clear cell carcinomas of the female genital tract, but HNF-1β is not.
Does Staged Breast Reduction before Nipple-Sparing Mastectomy Decrease Complications? A Matched Cohort Study between Staged and Nonstaged Techniques
Authors: Salibian Ara A. , Frey Jordan D. , Karp Nolan S. , Choi Mihye
Published: August 2019

Background:

Nipple-sparing mastectomy in patients with large, ptotic breasts is a reconstructive challenge. Staged breast reduction before prophylactic nipple-sparing mastectomy has been shown to decrease complications; however, a direct comparison of outcomes between staged and nonstaged techniques is lacking.

Methods:

A retrospective review of all patients that underwent staged breast reduction before nipple-sparing mastectomy was conducted. Staged cases were matched to nonstaged nipple-sparing mastectomy cases according to known risk factors for complications. Individual staged cases with appropriate matches in all these categories were then each paired to two nonstaged cases according to the nearest higher and lower mastectomy weight. Staged and nonstaged cohorts were compared with regard to demographics, operative characteristics, and reconstructive outcomes.

Results:

Eighteen staged breast reductions were identified, performed at an average of 5.0 months before nipple-sparing mastectomy. Staged reductions were matched to 36 prophylactic nonstaged reductions. Average combined mastectomy weight (breast reduction and mastectomy weight) in the staged group was significantly higher than in the nonstaged group (992.6 g versus 640 g; p = 0.0004), although isolated mastectomy weights were comparable (607.1 g versus 640.0 g, respectively; p = 0.6311). Major mastectomy flap necrosis rates were significantly lower in the staged cohort than in the nonstaged cohort (0 percent versus 22.2 percent, respectively; p = 0.0415). Rates of minor mastectomy flap necrosis, partial nipple necrosis, and explantation trended lower in the staged cohort.

Conclusion:

In patients with large breast size, staged breast reduction before nipple-sparing mastectomy had significantly lower rates of major flap necrosis compared with nonstaged cases after controlling for other known risk factors for complications.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, III.
Changing trends in proportional incidence and net survival of screened and nonscreened breast cancers among women in England
Authors: Wu Haiyan , Wong Kwok , Lu Shou-En , Broggio John , Zhang Lanjing
Published: August 2019

Background

Uptake of breast cancer screening has been decreasing in England since 2007, and may increase proportional incidence of nonscreened cancers. However, recent trends in proportional incidence and net-survivals of screened and nonscreened breast cancers are unclear.

Methods

We extracted population-based proportional incidence and age-standardized 5-year net-survivals from Public Health England, for English women with invasive breast cancer diagnosed during 1995-2011 (linked to death certificates, followed through 2016). Piecewise log-linear models with change-point/joinpoint were used to estimate temporal trends. We conducted a quasi-experimental study to test the hypothesis that the trend-change year of proportional incidence coincided with that of 5-year net-survival.

Results

Among 254,063 women in England with invasive breast cancer diagnosed during 1995-2011, there was downward-to-upward trend-change in proportional incidence of nonscreened breast cancers (annual percent change[APC]=5.6 after 2007 versus APC=-3.5 before 2007, P<0.001) in diagnosis-year 2007, when steeper upward-trend in age-standardized 5-year net survival started (APC=5.7 after 2007/2008 versus APC=0.3 before 2007/2008, P<0.001). Net-survival difference of screened versus nonscreened cancers also significantly narrowed (18% in 2007/2008 versus 5% in 2011). Similar associations were found in all strata of race, cancer stage, grade and histology, except in Black patients or patients with stage I, stage III, or grade I cancer.

Conclusions

The downward-to-upward trend-change in proportional incidence of nonscreened breast cancers is associated with steeper upward-trend in age-standardized 5-year net survival among English women in recent years. Survival benefits of breast cancer screening appear decreasing in recent years. The data support reduction of breast cancer screening in some patients.
Smoking, DNA methylation and lung function: a Mendelian randomization analysis to investigate causal relationships
Authors: Jamieson Emily , Korologou-Linden Roxanna , Wootton Robyn E. , Guyatt Anna L. , Battram Thomas , Burrows Kimberley , Gaunt Tom R. , Tobin Martin , Munafò Marcus , Smith George Davey , Tilling Kate , Relton Caroline , Richardson Tom G. , Richmond Rebecca C.
Published: August 2019

Whether smoking-associated DNA methylation has a causal effect on lung function has not been thoroughly evaluated. We investigated the causal effects of 474 smoking-associated CpGs on forced expiratory volume in one second (FEV1) in two-sample Mendelian randomization (MR) using methylation quantitative trait loci and genome-wide association data for FEV1. We found evidence of a possible causal effect for DNA methylation on FEV1 at 18 CpGs (p<1.2×10−4). Replication analysis supported a causal effect at three CpGs (cg21201401 (ZGPAT), cg19758448 (PGAP3) and cg12616487 (AHNAK) (p<0.0028). DNA methylation did not clearly mediate the effect of smoking on FEV1, although DNA methylation at some sites may influence lung function via effects on smoking. Using multiple-trait colocalization, we found evidence of shared causal variants between lung function, gene expression and DNA methylation. Findings highlight potential therapeutic targets for improving lung function and possibly smoking cessation, although large, tissue-specific datasets are required to confirm these results.
Complement-dependent synapse loss and microgliosis in a mouse model of multiple sclerosis
Authors: Hammond Jennetta W. , Bellizzi Matthew J. , Ware Caroline , Qiu Wen Q. , Saminathan Priyanka , Li Herman , Luo Shaopeiwen , Li Yuanhao , Gelbard Harris A.
Published: August 2019

Multiple sclerosis (MS) is an inflammatory, neurodegenerative disease of the CNS characterized by both grey and white matter injury. Microglial activation and a reduction in synaptic density are key features of grey matter pathology that can be modeled with experimental autoimmune encephalomyelitis (EAE). Complement deposition combined with microglial engulfment has been shown during normal development and in disease as a mechanism for pruning synapses. We tested whether there is excess complement production in the EAE hippocampus and whether complement-dependent synapse loss is a source of degeneration in EAE using C1qa and C3 knockout mice. We found that C1q and C3 protein levels were elevated in EAE mice. Genetic loss of C1qa provided a small degree of protection from EAE-induced decreases in synaptic density. However, C1qa knockout EAE mice had similar levels of microglial activation and identical clinical scores as WT EAE mice. C3 knockout mice were largely protected from EAE-induced synapse loss and microglial activation, results that correlated with a reduction in the EAE clinical score. Thus, pathologic expression and activation of the early complement pathway drives a portion of the synapse elimination observed in the EAE grey matter.
Translocational unfolding in clostridial binary iota toxin complex
Authors: Yamada Tomohiro , Yoshida Toru , Kawamoto Akihiro , Mitsuoka Kaoru , Iwasaki Kenji , Tsuge Hideaki
Published: August 2019

Protein translocation across the membrane is critical for microbial pathogenesis and various cellular functions. Bacterial binary toxins such as anthrax toxin are composed of enzyme components and a translocation channel, which catalyses substrate unfolding and translocation. Here we report the structures of the clostridial binary toxin (iota toxin) translocation channel Ib-pore and its complex with ADP-ribosyltransferase Ia. The Ib-pore structure at atomic resolution provides a similar structural framework as observed for the catalytic ϕ-clamp of the anthrax protective antigen pore. However, the Ia-bound Ib-pore structure showed a unique binding mode of Ia: one Ia binds to the Ib-pore, and the Ia N-terminal domain interacts with Ib via two other Ib-pore bottlenecks with multiple weak interactions. Furthermore, Ib-binding induces Ia N-terminal α-helix tilting and partial unfolding, whereupon the unfolded N-terminus continues to the ϕ-clamp gate. This study reveals the novel mechanism of N-terminal unfolding, which is crucial for protein translocation.
Functional characterization ofRalstonia insidiosa, a bona fide resident at the maternal-fetal interface
Authors: Parnell Lindsay A. , Willsey Graham G. , Joshi Chetanchandra S. , Yin Yin , Wargo Matthew J. , Mysorekar Indira U.
Published: August 2019

Controversy about whether there are microbes in the placenta and if they have any functional importance during pregnancy and for neonatal health is ongoing. Previous work has demonstrated that the basal plate (BP), comprising maternal and fetal derived cells harbors intracellular bacteria. 16S sequencing and bacterial species-specific analysis of term placentas revealed that the gram-negative bacillusRalstonia insidiosa, native to aqueous environments and an effective biofilm promoter, comprises the most abundant species in the BP. Here, we demonstrate whetherR. insidiosacells home to a particular niche in the BP, how they may arrive there, and whether they are associated with adverse outcomes. We developed methods to detect and study cell-specific localization ofR. insidiosausing ex vivo and in vitro models. Additionally, we studied potential routes ofR. insidiosaentry into the placenta. We show thatR. insidiosais a bona fide resident in human placental BP. It can access trophoblast cells in culture and within basal plate tissues where it localizes to intracellular single-membrane vacuoles and can replicate. However, the presence ofR. insidiosadoes not cause cell death and does not induce a pro-inflammatory immune response suggesting that it is not harmful in and of itself. Finally, we show that in a pregnant mouse model,R. insidiosatraffics to the placenta via the intrauterine route but does not induce preterm labor or preterm birth. Together, our findings provide a foundation for understanding non-pathogenic placental cell-microbe interactions and the functional importance ofR. insidiosain placental health and physiology.
Statistical inference for the evolutionary history of cancer genomes
Authors: Dinh K. N. , Jaksik R. , Kimmel M. , Lambert A. , Tavaré S.
Published: August 2019

Recent years have produced a large amount of work on inference about cancer evolution from mutations identified in cancer samples. Much of the modeling work has been based on classical models of population genetics, generalized to accommodate time-varying cell population size. Reverse-time genealogical views of such models, commonly known as coalescents, have been used to infer aspects of the past of growing populations. Another approach is to use branching processes, the simplest scenario being the linear birth-death process (lbdp), a binary fission Markov age-dependent branching process. A genealogical view of such models is also available. The two approaches lead to similar but not identical results. Inference from evolutionary models of DNA often exploits summary statistics of the sequence data, a common one being the so-called Site Frequency Spectrum (SFS). In a sequencing experiment with a known number of sequences, we can estimate for each site at which a novel somatic mutation has arisen, the number of cells that carry that mutation. These numbers are then grouped into sites which have the same number of copies of the mutant. SFS can be computed from the statistics of mutations in a sample of cells, in which DNA has been sequenced. In this paper, examine how the SFS based on birth-death processes differ from those based on the coalescent model. This may stem from the different sampling mechanisms in the two approaches. However, we also show mathematically and computationally that despite this, they can be made quantitatively comparable at least for the range of parameters typical for tumor cell populations. We also present a model of tumor evolution with selective sweeps, based on coalescence, and demonstrate how it may help in understanding the past history of tumor as well the influence of data pre-processing. We illustrate the theory with applications to several examples of The Cancer Genome Atlas tumors.
Validating the Cyc2 neutrophilic Fe oxidation pathway using meta-omics of Zetaproteobacteria iron mats at marine hydrothermal vents
Authors: McAllister Sean M. , Polson Shawn W. , Butterfield David A. , Glazer Brian T. , Sylvan Jason B. , Chan Clara S.
Published: August 2019

Zetaproteobacteria create extensive iron (Fe) oxide mats at marine hydrothermal vents, making them an ideal model for microbial Fe oxidation at circumneutral pH. Comparison of neutrophilic Fe-oxidizer isolate genomes has revealed a hypothetical Fe oxidation pathway, featuring a homolog of the Fe oxidase Cyc2 from Acidithiobacillus ferrooxidans. However, Cyc2 function is not well verified in neutrophilic Fe-oxidizers, particularly in Fe-oxidizing environments. Toward this, we analyzed genomes and metatranscriptomes of Zetaproteobacteria, using 53 new high-quality metagenome assembled genomes reconstructed from Fe mats at Mid-Atlantic Ridge, Mariana Backarc, and Loihi Seamount (Hawaii) hydrothermal vents. Phylogenetic analysis demonstrated conservation of Cyc2 sequences among most neutrophilic Fe-oxidizers, suggesting a common function. We confirmed the widespread distribution of cyc2 and other model Fe oxidation pathway genes across all represented Zetaproteobacteria lineages. High expression of these genes was observed in diverse Zetaproteobacteria under multiple environmental conditions, and in incubations. The putative Fe oxidase gene, cyc2, was highly expressed in situ, often as the top expressed gene. The cyc2 gene showed increased expression in Fe(II)-amended incubations, with corresponding increases in carbon fixation and central metabolism gene expression. These results substantiate the Cyc2-based Fe oxidation pathway in neutrophiles and demonstrate its significance in marine Fe-mineralizing environments.
Intraspecific difference among herbivore lineages and their host-plant specialization drive the strength of trophic cascades
Authors: Sentis Arnaud , Bertram Raphaël , Dardenne Nathalie , Simon Jean-Christophe , Magro Alexandra , Pujol Benoit , Danchin Etienne , Hemptinne Jean-Louis
Published: August 2019

Abstract

Trophic cascades—the indirect effect of predators on non-adjacent lower trophic levels—are important drivers of the structure and dynamics of ecological communities. However, the influence of intraspecific trait variation on the strength of trophic cascade remains largely unexplored, which limits our understanding of the mechanisms underlying ecological networks. Here we experimentally investigated how intraspecific difference among herbivore lineages specialized on different host plants influences the strength of trophic cascade in a terrestrial tritrophic system. We found that the occurrence and strength of the trophic cascade are strongly influenced by herbivores’ lineage and host-plant specialization but are not associated with density-dependent effects mediated by the growth rate of herbivore populations. Our findings stress the importance of intraspecific heterogeneities and evolutionary specialization as drivers of the strength of trophic cascades and underline that intraspecific variation should not be overlooked to decipher the joint influence of evolutionary and ecological factors on the functioning of multi-trophic interactions.
Predictive coding account of action perception: Evidence from effective connectivity in the Action Observation Network
Authors: Urgen Burcu A. , Saygin Ayse P.
Published: August 2019

Visual perception of actions is supported by a network of brain regions in the occipito-temporal, parietal, and premotor cortex in the primate brain, known as the Action Observation Network (AON). Although there is a growing body of research that characterizes the functional properties of each node of this network, the communication and direction of information flow between the nodes is unclear. According to the predictive coding account of action perception, this network is not a purely feedforward system but has feedback connections through which prediction error signals are communicated between the regions of the AON. In the present study, we investigated the effective connectivity of the AON in an experimental setting where the human subjects’ predictions about the observed agent were violated, using fMRI and Dynamical Causal Modeling (DCM). We specifically examined the influence of the lowest and highest nodes in the AON hierarchy, pSTS and ventral premotor cortex, respectively, on the middle node, inferior parietal cortex during prediction violation. Our DCM results suggest that the influence on the inferior parietal node is through a feedback connection from ventral premotor cortex during perception of actions that violate people’s predictions.
Assembly methods for nanopore-based metagenomic sequencing: a comparative study
Authors: Latorre-Pérez Adriel , Villalba-Bermell Pascual , Pascual Javier , Porcar Manuel , Vilanova Cristina
Published: August 2019

Background

Metagenomic sequencing has lead to the recovery of previously unexplored microbial genomes. In this sense, short-reads sequencing platforms often result in highly fragmented metagenomes, thus complicating downstream analyses. Third generation sequencing technologies, such as MinION, could lead to more contiguous assemblies due to their ability to generate long reads. Nevertheless, there is a lack of studies evaluating the suitability of the available assembly tools for this new type of data.

Findings

We benchmarked the ability of different short-reads and long-reads tools to assembly two different commercially available mock communities, and observed remarkable differences in the resulting assemblies depending on the software of choice. Short-reads metagenomic assemblers proved unsuitable for MinION data. Among the long-reads assemblers tested, Flye and Canu were the only ones performing well in all the datasets. These tools were able to retrieve complete individual genomes directly from the metagenome, and assembled a bacterial genome in only two contigs in the best scenario. Despite the intrinsic high error of long-reads technologies, Canu and Flye lead to high accurate assemblies (~99.4-99.8 % of accuracy). However, errors still had an impact on the prediction of biosynthetic gene clusters.

Conclusions

MinION metagenomic sequencing data proved sufficient for assembling low-complex microbial communities, leading to the recovery of highly complete and contiguous individual genomes. This work is the first systematic evaluation of the performance of different assembly tools on MinION data, and may help other researchers willing to use this technology to choose the most appropriate software depending on their goals. Future work is still needed in order to assess the performance of Oxford Nanopore MinION data on more complex microbiomes.
Iron chelation by curcumin suppress both curcumin-induced autoghagy and cell death together with iron overload neoplastic transformation
Authors: Rainey Nathan E. , Moustapha Aoula , Saric Ana , Nicolas Gael , Sureau Franck , Petit Patrice X.
Published: August 2019

Iron overload, notably caused by hereditary hemochromatosis, is an excess storage of iron in various organs which cause tissue damage and may promote tumorigenesis. To manage that disorder, free iron depletion can be induced by iron chelators like deferoxamine which are gaining interest also in the cancer field since iron stock could be a potent target for managing tumorigenesis. Curcumin, a well-known active substance extracted from the turmeric rhizome, has shown to be destabilizing endoplasmic reticulum and secondarily lysozomes, increasing mitophagy/autophagy and subsequent apoptosis. Recent findings show that cells treated with curcumin exhibit also a decrease in ferritin, which is consistent with it’s chemical structure and iron chelating activity. Here we investigated how curcumin would play on the intracellular effects of iron overload via Fe-Nitriloacetic acid or Ferric ammonium citrate loading in Huh-7 cells and explore consequences in terms of antioxidant activity, autophagy, or apoptotic signal transduction. With T51B and RL-34 epithelial cells experiments, we brought evidence that curcumin-iron complexation abolishes both curcumin-induced autophagy and apoptosis together with the tumorigenic action of iron overload.
MADS-box factor AGL16 negatively regulates drought resistance via stomatal density and stomatal movement
Authors: Zhao Ping-Xia , Miao Zi-Qing , Zhang Jing , Liu Qian-Qian , Xiang Cheng-Bin
Published: August 2019

Drought is one of the most severe environmental factors limiting plant growth and productivity. Plants respond to drought by closing stomata to reduce water loss. The molecular mechanisms underlying plant drought resistance are very complex and yet to be fully understood. While much research attention has been focused on the positive regulation of stomatal closure, less is known about its negative regulation, equally important in this reversible process. Here we show that the MADS-box transcriptional factor AGL16 acts as a negative regulator in drought resistance by regulating both stomatal density and movement. Loss-of-function mutantagl16was more resistant to drought stress with higher relative water content, which was attributed to a reduced leaf stomatal density and more sensitive stomatal closure due to a higher leaf ABA level compared with wild type, whileAGL16overexpression lines displayed the opposite phenotypes.AGL16is preferentially expressed in guard cells and down regulated in response to drought stress. The expression ofCYP707A3andAAO3in ABA metabolism andSDD1in stomatal development was altered by AGL16 as shown inagl16and overexpression lines. Chromatin immunoprecipitation, transient transactivation, and yeast-one-hybrid assays demonstrated that AGL16 bound the CArG motif in the promoter of theCYP707A3,AAO3, andSDD1to regulate their transcription, and therefore alter leaf stomatal density and ABA level. Taken together, AGL16 acts as a negative regulator of drought resistance by modulating leaf stomatal density and ABA accumulation.
Screening the MMV Open Access Pathogen box unveils novel and potent inhibitors of Amoebiasis agent: Entamoeba histolytica
Authors: Toghueo Rufin Marie Kouipou , Dize Darline , Laleu Benoît , Fokou Patrick Valere Tsouh , Kemgne Eugenie Aimee Madiesse , Boyom Fabrice Fekam
Published: August 2019

Amoebiasis caused by the protozoan parasite Entamoeba histolytica remains a major public health hazard, as being the second cause of death among parasitic infections. Although currently prescribed drugs have shown to be effective in the treatment of amoebiasis, side effects and emergence of parasites resistance prompted the search for novel drug to control this disease. In this regard, the Medicines for Malaria Venture (MMV) Pathogen Box library of selected compounds was screened to identify anti-Entamoeba histolytica agents using the resazurin based fluorescence assay. Overall, the results revealed three novel anti-Entamoeba histolytica scaffolds with low micromolar activity including MMV675968 (IC50 = 2.10 µM), MMV688179 (IC50 = 2.38 µM) and MMV688844 (IC50 = 5.63 µM). Structure-Activity-Relationship (SAR) studies led to identification of two analogs ∼100 fold more potent and selective than the original hit compound 1 (MMV675968): 1k (IC50 = 0.043 µM) and 1l (IC50 = 0.055 µM). Predictive analysis using Maestro 11.6 suggested that these hit compounds possess acceptable physicochemical and metabolism properties. These lead compounds are therefore good starting points for lead optimization studies towards identification of drug candidate against amoebiasis.

Author Summary

Diarrhoea is a leading cause of death for millions of children worldwide. One of the top 15 causes of severe diarrhoea is Entamoeba histolytica, causing amoebiasis. What makes E. histolytica dangerous is its ability to disseminate easily through a given population via contaminated food and water supplies. Moreover, E. histolytica is quite comfortable in the environment, difficult to kill with chorine and infect people at a very low dose, making it a priority pathogen to eradicate. Many drugs have been developed so far to cure this infection. However, they are not efficient enough to control the disease due to pathogen resistance that is becoming a big issue. In addition to that, almost all the drugs in use are highly toxic to human causing several side effects upon medications. Therefore, new, more efficient and less toxic drugs are urgently needed for the better management of amoebiasis. Since the development of a new drug takes years, repurposing existing drugs has been shown to shortcut the process and boost the discovery rate of new medicines. Using this same approach, we have identified two compounds that potently inhibit E. histolytica and are nontoxic that can enter the drug discovery pipeline for new amoebicidal drug development. Moreover, these new inhibitors could also serve as starting points for the synthesis of a library of amoebicidal compounds.
Case-Base-Control designs
Authors: Elhezzani Najla Saad , Bergsma Wicher , Weale Mike
Published: August 2019

Most genome-wide association studies (GWASs) use randomly selected samples from the population (hereafter bases) as the control set. This approach is successful when the trait of interest is rare; otherwise, a loss in the statistical power to detect disease-associated variants is expected. To address this, a proposal to combine the three sample types, cases, controls and bases is introduced, for instances when the disease under study is prevalent. This is done by modelling the bases as a mixture of multinomial logistic functions of cases and controls, according to the disease prevalence. The maximum likelihood method is used to estimate the underlying parameters using the EM algorithm. Three classical tests of association; score, Walds, and likelihood ratio tests are derived and their power of detecting genetic associations under different designs is compared. Simulations show that combining the three samples can increase the power to detect disease-associated variants, though a very large base sample set can compensate for the lack of controls.
Investigation of diffusion alloying time on electrochemical behavior and conductivity of Nb-modified AISI 430 SS as PEMFC bipolar plate
Authors: Cheng Fupeng , Cui Jinglong , Xu Shuai , Wang Hongyu , Zhang Pengchao , Sun Juncai
Published: August 2019

Purpose

The purpose of this paper is to improve the surface electrical conductivity and corrosion resistance of AISI 430 stainless steel (430 SS) as bipolar plates for proton exchange membrane fuel cells (PEMFCs), a protective Nb-modified layer is formed onto stainless steel via the plasma surface diffusion alloying method. The effect of diffusion alloying time on electrochemical behavior and surface conductivity is evaluated.

Design/methodology/approach

In this work, the surface electrical conductivity and corrosion resistance of modified specimen are evaluated by the potentiodynamic and potentionstatic polarization tests. Moreover, the hydrophobicity is also investigated by contact angle measurement.

Findings

The Nb-modified 430 SS treated by 1.5 h (1.5Nb) presented a lower passivation current density, lower interfacial contact resistance and a higher hydrophobicity than other modified specimens. Moreover, the 1.5 Nb specimen presents a smoother surface than other modified specimens after potentionstatic polarization tests.

Originality/value

The effect of diffusion alloying time on electrochemical behavior, surface conductivity and hydrophobicity of modified specimen is evaluated. The probable anti-corrosion mechanism of Nb-modified specimen in simulated acid PEMFC cathode environment is presented.
Influence of Big Data in managing cyber assets
Authors: Mitra Amit , Munir Kamran
Published: August 2019

Purpose

Today, Big Data plays an imperative role in the creation, maintenance and loss of cyber assets of organisations. Research in connection to Big Data and cyber asset management is embryonic. Using evidence, the purpose of this paper is to argue that asset management in the context of Big Data is punctuated by a variety of vulnerabilities that can only be estimated when characteristics of such assets like being intangible are adequately accounted for.

Design/methodology/approach

Evidence for the study has been drawn from interviews of leaders of digital transformation projects in three organisations that are within the insurance industry, natural gas and oil, and manufacturing industries.

Findings

By examining the extant literature, the authors traced the type of influence that Big Data has over asset management within organisations. In a context defined by variability and volume of data, it is unlikely that the authors will be going back to restricting data flows. The focus now for asset managing organisations would be to improve semantic processors to deal with the vast array of data in variable formats.

Research limitations/implications

Data used as evidence for the study are based on interviews, as well as desk research. The use of real-time data along with the use of quantitative analysis could lead to insights that have hitherto eluded the research community.

Originality/value

There is a serious dearth of the research in the context of innovative leadership in dealing with a threatened asset management space. Interpreting creative initiatives to deal with a variety of risks to data assets has clear value for a variety of audiences.
Job insecurity and impression management
Authors: Probst Tahira M. , Jiang Lixin , López Bohle Sergio Andrés
Published: August 2019

Purpose

The purpose of this paper is to test competing models of the relationship between job insecurity and two forms of impression management (self- and supervisor-focused) on job performance. Specifically, does job insecurity lead to greater subsequent impression management; or, does preventative use of impression management subsequently lead to reductions in job insecurity? Additionally, how do these both relate to in-role performance?

Design/methodology/approach

Using two-wave survey data collected from 184 working adults in the USA and the two-step approach recommended by Cole and Maxwell (2003) and Taris and Kompier (2006), the authors tested cross-lagged relationship between job insecurity and both forms of impression management by comparing four different models: a stability model, a normal causation model (with cross-lagged paths from T1 job insecurity to T2 impression management), a reversed causation model (with cross-lagged paths from T1 impression management to T2 job insecurity) and a reciprocal causation model (with all cross-lagged paths described in the normal and reversed causation model).

Findings

Results were supportive of the reversed causation model which indicated that greater use of supervisor-focused impression management at Time 1 predicted lower levels of job insecurity at Time 2 (after controlling for prior levels of job insecurity); moreover, job insecurity at Time 1 was then significantly associated with more positive in-role behaviors at Time 2. Moreover, the test of the indirect effect between T1 impression management and T2 performance was significant.

Originality/value

These results suggest that impression management clearly plays an important role in understanding the relationship between job insecurity and job performance. However, employees appear to utilize impression management as a means of pre-emptively enhancing their job security, rather than as a tool to reactively cope with perceived job insecurity.
Design and application of integrated parabolic soft actuator
Authors: Liu Dong , Wang Minghao , Cong Ming
Published: August 2019

Purpose

The purpose of this paper is to solve the common problems of outer phenomenon and stress concentration among pneumatic networks soft actuators.

Design/methodology/approach

On the basis of imitating the caterpillar structure, the new soft actuator adopts the integral circular ladder structure instead of the traditional independent distributed structure as the air chamber. Through the comparison of several different structures, the parabolic in-wall curve is found to be fit for designing the optimal integrated chamber structure of the soft actuator. The curve function of each ladder chamber is computed based on the torque distribution model, aiming to decrease the terminal deformation. Meanwhile, the FEM analysis method is applied to establish the motion model of the integrated parabolic ladder soft actuator. The model’s accuracy, as well as structure’s deformation and stress, are verified.

Findings

Compared with the FEM data, the experimental data indicate that the new soft actuator has no obvious outer phenomenon, the maximum stress decreases and the stiffness increases. The new actuator is applied for designing a flexible gripper to grasp objects of different shapes and sizes. The gripper can grasp objects of 52.6 times its own mass.

Practical implications

The designed gripper is available for flexible production in various fields, such as capturing fruits of different sizes, soft foods or parts with complex shapes.

Originality/value

This paper proposes a new type soft actuator, which provides a solution for exploring the field of the soft robot. The problems of outer phenomenon and stress concentration are suppressed with pneumatic networks soft actuators.
Research on impact evaluation of academic journals from multidimensional perspective
Authors: Zhao Rongying , Wang Xu
Published: August 2019

Purpose

The purpose of this paper is to introduce altmetric indicators and combine with traditional citation indicators to comprehensively evaluate the impact of academic journals from the perspective of multidimensional and multi-indicator fusion.

Design/methodology/approach

The authors take international multidisciplinary journals as an example, combining 14 traditional citation indicators of academic journals and introducing 14 altmetric indicators to build a comprehensive evaluation model of the impact of academic journals (academic impact and societal impact). At the same time, the authors systematically construct a journal evaluation indicator system from three dimensions. Then, the indicators data of three dimensions are evaluated by normalized processing, correlation analysis, reliability and validity analysis, PCA and factor analysis.

Findings

Two-dimensional and three-dimensional analyses can exactly provide some useful information for academic journals’ location in the respective coordinate systems. There are strong positive correlations among the measured indicators in the three dimensions, and each indicator has a significant consistency between whole and internal. The correlation coefficient between FD1 and FD2 is 0.888 with a strong positive correlation. It shows that the traditional citation indicators provided by WoS and Scopus database are highly consistent, and they are comparable and alternative in evaluating the academic impact of journals. The correlation coefficients of FD1, FD2 with FD3 are 0.831 and 0.798. There are strong positive correlations among them, which indicate that the evaluation of journals’ societal impact based on altmetrics indicator can be considered as a potential supplement to academic impact evaluation based on citation and to reflect the multidimensional nature of journals impact in an immediate way.

Originality/value

Multidimensional and multi-indicator perspective evaluation can provide references for the selection of impact evaluation indicators and model optimization of academic journals, and also provide new ideas for improving the status of the impact evaluation of academic journals.
Low frequency sound insulation performance of asymmetric coupled-membrane acoustic metamaterials
Authors: Cai Mengna , Tian Hongyan , Liu Haitao , Qie Yanhui
Published: August 2019

Purpose

With the development of the modern technology and aerospace industry, the noise pollution is remarkably affecting people’s daily life and has been become a serious issue. Therefore, it is the most important task to develop efficient sound attenuation barriers, especially for the low-frequency audible range. However, low-frequency sound attenuation is usually difficult to achieve for the constraints of the conventional mass-density law of sound transmission. The traditional acoustic materials are reasonably effective at high frequency range. This paper aims to discuss this issue.

Design/methodology/approach

Membrane-type local resonant acoustic metamaterial is an ideal low-frequency sound insulation material for its structure is simple and lightweight. In this paper, the finite element method is used to study the low-frequency sound insulation performances of the coupled-membrane type acoustic metamaterial (CMAM). It consists of two identical tensioned circular membranes with fixed boundary. The upper membrane is decorated by a rigid platelet attached to the center. The sublayer membrane is attached with two weights, a central rigid platelet and a concentric ring with inner radius e. The influences of the distribution and number of the attached mass, also asymmetric structure on the acoustic attenuation characteristics of the CMAM, are discussed.

Findings

In this paper, the acoustic performance of asymmetric coupled-membrane metamaterial structure is discussed. The influences of mass number, the symmetric and asymmetry structure on the sound insulation performance are analyzed. It is shown that increasing the number of mass attached on membrane, structure exhibits low-frequency and multi-frequency acoustic insulation phenomenon. Compared with the symmetrical structure, asymmetric structure shows the characteristics of lightweight and multi-frequency sound insulation, and the sound insulation performance can be tuned by adjusting the distribution mode and location of mass blocks.

Originality/value

Membrane-type local resonant acoustic metamaterial is an ideal low-frequency sound insulation material for its structure is simple and lightweight. How to effectively broaden the acoustic attenuation band at low frequency is still a problem. But most of researchers focus on symmetric structures. In this study, the asymmetric coupled-membrane acoustic metamaterial structure is examined. It is demonstrated that the asymmetric structure has better sound insulation performances than symmetric structure.