bluuebunny/crossref_metadata_2025 huggingface dataset:
Qualitative Analysis of Solid Phase Synthesis Reaction Products by X-ray Spectrometry
Authors: Carlton Robert A. , Orton Edward , Lyman Charles E. , Roberts James E.
Published: May 2019

Abstract: A novel method for the synthesis of polypeptides using polystyrene/divinylbenzene copolymers as solid supports has drawn the attention of medicinal, pharmaceutical, and agricultural chemists because of its utility in combinatorial chemistry and parallel synthesis. In this method, arrays of solid-phase organic synthesis experiments are conducted simultaneously thereby enabling the preparation of large numbers of novel compounds over a short time period. The analysis of organic compounds attached to polymer supports presents unique challenges to chemists. This study presents some results of the application of energy-dispersive X-ray spectrometry (EDS) in the environmental scanning electron microscope (ESEM) to this problem. EDS in the ESEM has the advantages of minimal sample size, speed, and simplicity because the analyses are performed without special specimen preparation. The progress of a two-step synthetic transformation was followed using EDS-ESEM by the presence of a sulfur peak in the first synthetic step and by a bromine peak in the second step. The synthetic products were also evaluated by infrared spectroscopy and by elemental analysis (ion chromatography). The agreement of the qualitative analysis among all three techniques was good. Analysis by EDS-ESEM not only complements current analytical techniques in solid phase synthesis; it also provides insight into the details of the synthetic transformation.
Energy-Loss Measurements of Polymer Microstructure and Polymer Interfaces: Issues and Opportunities
Authors: Siangchaew K. , Libera M.
Published: May 2019

Abstract: The traditional methods for studying polymer microstructure in the transmission electron microscope largely hinge on the use of differential heavy-element staining to induce amplitude contrast. However, adequate staining agents are not available for all polymer systems. Furthermore, nonlinearities in the distribution of stain, particularly at interfaces, degrade the achievable resolution. Spatially resolved electron energy loss spectroscopy (EELS), on the other hand, provides a new opportunity to study polymer microstructure by providing rich spectroscopic features and high spatial resolution. Translating this opportunity into practice is underpinned by three main factors: (1) the availability of spectral fingerprints distinguishing various polymers; (2) the limits of achievable resolution; and (3) the ultimate constraints imposed by electron irradiation. This study discusses these issues and demonstrates the use of spatially resolved EELS with examples from hydrocarbon homopolymer and homopolymer blends of polyphenylene sulfide (PPS) and polyethylene terephthalate (PET), nylon 6/high-density polyethylene (HDPE) and polystyrene/polyethylene (PS/PE).
Coupling landscapes and river flows to restore highly modified rivers
Authors: Whipple A. A. , Viers J. H.
Published: May 2019

Modifications to landscapes and flow regimes of rivers have altered the function, biodiversity, and productivity of freshwater ecosystems globally. Reestablishing geomorphological and hydrological conditions necessary to sustain ecosystems is a central challenge for restoration within highly altered systems. Meeting this challenge requires simultaneously addressing multiple and interacting stressors within the context of irreversible changes and socio‐economic constraints. Traditionally, river restoration approaches either physically change the landscape or channel (channel‐floodplain manipulation) or adjust hydrology (environmental flows), and such actions are often independent. We juxtapose these two subfields of river restoration, which have undergone parallel transformations, from goals of reproducing static representations of form and flow regime to goals of reestablishing processes. The parallel transformations have generated shared ideas, which point to benefits of coupling channel‐floodplain manipulation and environmental flow actions to achieve process‐based goals. Such coupling supports comprehensive river restoration efforts aimed at supporting resilient ecosystems within human dominated landscapes in a nonstationary climate. We identify four elements of coupled approaches for restoring highly modified rivers: (1) identify physical and ecological process potential given interactive effects of altered landscapes and flows; (2) consider capacity for sustaining identified processes under potential future change; (3) model alternatives for coupled restoration actions to support identified processes; and (4) evaluate alternatives using metrics representing integrative effects of coupled actions. We suggest these emergent elements contribute to the development of standard practices for restoring highly modified rivers and encourage an increasing number and quality of coupled applications.
The Blob Causing Earthquakes
Authors: Joel Lucas
Published: May 2019

Geophysicists discover that a “blob” of rock sinking into the mantle is the force triggering earthquakes in the Hindu Kush.
Effects of an Explosive Polar Cyclone Crossing the Antarctic Marginal Ice Zone
Authors: Vichi Marcello , Eayrs Clare , Alberello Alberto , Bekker Anriëtte , Bennetts Luke , Holland David , de Jong Ehlke , Joubert Warren , MacHutchon Keith , Messori Gabriele , Mojica Jhon F. , Onorato Miguel , Saunders Clinton , Skatulla Sebastian , Toffoli Alessandro
Published: May 2019

Antarctic sea ice shows a large degree of regional variability, which is partly driven by severe weather events. Here we bring a new perspective on synoptic sea ice changes by presenting the first in situ observations of an explosive extratropical cyclone crossing the winter Antarctic marginal ice zone (MIZ) in the South Atlantic. This is complemented by the analysis of subsequent cyclones and highlights the rapid variations that ice‐landing cyclones cause on sea ice: Midlatitude warm oceanic air is advected onto the ice, and storm waves generated close to the ice edge contribute to the maintenance of an unconsolidated surface through which waves propagate far into the ice. MIZ features may thus extend further poleward in the Southern Ocean than currently estimated. A concentration‐based MIZ definition is inadequate, since it fails to describe a sea ice configuration which is deeply rearranged by synoptic weather.
Epoxy/methyl methacrylate acrylonitrile butadiene styrene (MABS) copolymer blends: reaction-induced viscoelastic phase separation, morphology development and mechanical properties
Authors: Joy Jomon , Winkler Krzysztof , Joseph Kuruvilla , Anas S. , Thomas Sabu
Published: May 2019

Epoxy/MABS blends undergo viscoelastic phase separation during curing due to the dynamic asymmetry of the phases and a significant improvement in the mechanical properties of the system is observed.
Outage performance of NOMA‐based integrated satellite‐terrestrial networks with imperfect CSI
Authors: Xie Silin , Zhang Bangning , Guo Daoxing , Ma Wenfeng
Published: May 2019

In this Letter, the authors consider the integrated satellite‐terrestrial networks with non‐orthogonal multiple access (NOMA) scheme, where the satellite communicates with users through a decode‐and‐forward relay. The impact of imperfect channel state information (CSI) is studied by adopting a pilot‐based channel estimation. Closed‐form outage probability expressions for each NOMA user are derived, as well as asymptotic expressions at high signal‐to‐noise ratio region. Simulation is implemented to confirm the validity of theoretical results and the superiority of the proposed NOMA scheme.
Injection‐locked frequency divider with a hybrid 3D multi‐path and single‐path inductor
Authors: Jang Sheng‐Lyang , Lu Chien‐Hsing , Yang Jia‐Ching
Published: May 2019

This Letter proposes a divide‐by‐2 injection‐locked frequency divider (ILFD) with a new passive resonator. The ILFD in the 0.18 μm 1P6M CMOS process uses a three‐dimensional inductor consisted of three series single‐path and multi‐path inductors. Measured data shows that the varactor‐less divide‐by‐2 ILFD has wide locking range, low power consumption and occupies a small area of 0.4446 × 0.9198 mm2.
Combining colour and grey‐level co‐occurrence matrix features: a comparative study
Authors: Khaldi Belal , Aiadi Oussama , Kherfi Mohammed Lamine
Published: May 2019

Grey‐level co‐occurrence matrix (GLCM) is a widely used texture feature descriptor that is extracted from grey‐level images. A considerable amount of work in the literature has been done trying to combine colour with GLCM features. The aim of this study is to examine the effect of integrating colour with GLCM. To this end, 14 descriptors that have been proposed in literature based on different colour combining approaches, four Convolutional Neural Networks‐based, two aggregation‐based, and five other handcrafted descriptors have been engaged in this comparison. Five widely known data sets have been used to experimentally evaluate each descriptor. The evaluation has been conducted for image classification and image retrieval. Results indicated that there is no co‐occurrence‐matrix‐based descriptor that overcomes all the others in all data sets. Nevertheless, some descriptors have shown a remarkably higher performance than the others.
Implementation of a common grounded Z‐source DC–DC converter with improved operation factors
Authors: Rostami Sajad , Abbasi Vahid , Blaabjerg Frede
Published: May 2019

This study proposes a common grounded Z‐source DC–DC converter. In comparison with a conventional Z‐source converter, it converts voltage with higher voltage gain and lower voltage stress on the switch and diodes that means an improvement in efficiency. In addition, increasing the duty cycle reduces its output voltage ripple percentage that improves its operation quality. The converter is analysed and compared with other converters. Its main equations are obtained, which show the converter advantages as lower voltage stress, smaller inductors and higher voltage gain in comparison with the reviewed converters. A prototype for the proposed converter is prepared based on analysis and theoretical parts. Experiments are done along with the analysis. Experimental results and theoretical equations are used to show the converter advantages.
Exponential frequency correlation function and its application in Doppler shift estimation
Authors: Liu Lubo , Zhang Lu , Yu Tao , Ji Yuandong
Published: May 2019

A Doppler shift estimation problem of a noisy received signal consisting of multiple moving targets that have similar radial velocities is addressed here. Traditional Doppler shift estimation algorithms based on Fourier transform (FT) frequently exhibit low resolution. Here, an exponential frequency correlation function (EFCF) is proposed by introducing a sensitivity exponent p that controls its output signal‐to‐noise ratio (SNR) and velocity resolution into the expression of a classical frequency correlation function (FCF). On the basis of the proposed EFCF, a novel Doppler shift estimation algorithm can adaptively select the exponent of the EFCF to achieve the optimum Doppler shift estimation effect in an echo signal based on the elimination algorithm. Moreover, the proposed method is performed on the basis of the fast FT and product operation. Thus, it can be easily implemented. Numerical simulations demonstrate that the performance of the proposed method is significantly improved compared with the existing algorithms.
GPS/DVL/MEMS‐INS smartphone sensors integrated method to enhance USV navigation system based on adaptive DSFCF
Authors: Mostafa Mohamed Z. , Khater Hatem A. , Rizk Mohamed R. , Bahasan Abdullah M.
Published: May 2019

Although the inertial navigation system (INS) can provide a continuous navigation solution for most of unmanned surface vehicles (USVs), its reliability decreases over time due to the accelerometer and gyroscope drifts. The authors’ study introduces a novel method based on integrated micro electric mechanical system (MEMS)‐INS smartphone sensors with global positioning system (GPS) and Doppler velocity log (DVL). Since the GPS and DVL are used as reference systems to correct MEMS‐INS errors, their accuracies are decreased due to the bad weather and the noise of DVL, which effect on the efficiency of a whole navigation system. To resolve this problem, the adaptive data sharing factor combined filter (DSFCF) is used as integrated method. According to adaptive DSFCF integrated method, the reference system which has the beast accuracy is used to correct the USV navigation errors, and at the same time the least accuracy system will be detected and avoided. The proposed GPS/DVL/MEMS‐INS using adaptive DSFCF integrated method was tested on a surface reference trajectory in Mukalla city‐Yemen. The estimated results by this proposed method could provide a reliable navigation solution and give the least error compared by the GPS/DVL/MEMS‐INS Centralised Kalman filter and the GPS/DVL/MEMS‐INS constant DSFCF integrated methods.
Integration of non‐isolated DC–DC converters in battery storage systems – a topological exploration
Authors: Khanaki Razieh , Walker Geoffrey R. , Broadmeadow Mark A H. , Ledwich Gerard F.
Published: May 2019

This paper presents a topological exploration and evaluation of modularised battery systems with integrated non‐isolated DC–DC converters (battery‐integrated‐converters). Converter requirements for battery operation in charging/discharging, charge balance, bypass, and pass‐through modes have been considered. Topological variations have been derived to permit all battery operation modes. Design considerations and equations for each topology have been presented. The topological requirements have been summarised in tabular form with a 380 V bus storage system case study presented to demonstrate application of the design consideration discusses to a typical battery system specification. The comparison shows the buck, boost, and non‐inverting buck‐boost‐based converters are all similarly suitable, and other performance metrics are likely to determine the best choice for a given set of circumstances.
Ultrasound‐assisted synthesis of porous Mg(OH)2 nanostructures using hypersaline brine
Authors: Yousefi Sadegh , Ghasemi Behrooz
Published: May 2019

In this work, synthesis and formation of porous magnesium hydroxide (MH) nanostructures were investigated by chemical precipitation and sonochemical method using hypersaline brine containing large amounts of CaCl2, MgCl2, NaCl and KCl. The effect of ultrasound waves was investigated on the morpho‐structural, surface and thermal properties were investigated by means of X‐ray diffraction, field emission scanning electron microscopy, transmission electron microscopy, energy dispersive X‐ray spectrometer, Brunauer–Emmett–Teller and thermogravimetry‐differential thermal analysis techniques. It was indicated that ultrasound waves decreased grain and particle sizes of the sample which synthesised by sonochemical route (MH‐U). The MH‐U sample had a higher surface area, lower particle size, better particle distribution and lower transition temperature of MH to MgO.
Simulation study on piezoelectric characteristics of two‐dimensional ZnO nanodiscs
Authors: Yang Dechao , Qiu Yu , Fang Shengli , Song Wenbin
Published: May 2019

Two‐dimensional (2D) zinc oxide (ZnO) nanostructures have emerged as an attractive approach for constructing high‐performance piezoelectric nanogenerators (NGs) because of their high rate of surface area to volume and good mechanical durability for applications in energy conversion devices. However, there has been to date no comprehensive study on piezoelectric characteristics of 2D ZnO nanostructures. In this paper, 2D nanodiscs have been prepared by aqueous solution method on flexible indium tin oxide coated polyethylene terephthalate substrates. Also, the piezoelectric characteristics are statistically demonstrated and analysed on the as‐grown 2D ZnO nanodiscs by applying different external force with the finite element method (COMSOL Multiphysics). Besides, the size‐dependent simulation analysis of piezopotentials is also conducted for further optimising output performance of NGs based on 2D ZnO nanostructures. Also, the simulation will provide a guideline for designing high‐performance piezo‐nanodevices.
Updated orbital ephemeris of the ADC source X 1822-371: a stable orbital expansion over 40 years
Authors: Mazzola S. M. , Iaria R. , Di Salvo T. , Gambino A. F. , Marino A. , Burderi L. , Sanna A. , Riggio A. , Tailo M.
Published: May 2019

Aims. Source X 1822-371 is an eclipsing compact binary system with a period close to 5.57 h and an orbital period derivative Ṗorb of 1.51(7)×10−10 s s−1. The very high value of Ṗorb is compatible with a super-Eddington mass transfer rate from the companion star, as suggested by X-ray and optical data. The XMM-Newton observation taken in 2017 allows us to update the orbital ephemeris and verify whether the orbital period derivative has been stable over the past 40 yr.

Methods. We added two new values obtained from the Rossi-XTE (RXTE) and XMM-Newton observations performed in 2011 and 2017, respectively, to the X-ray eclipse arrival times from 1977 to 2008. We estimated the number of orbital cycles and the delays of our eclipse arrival times spanning 40 yr, using as reference time the eclipse arrival time obtained from the RXTE observation taken in 1996.

Results. Fitting the delays with a quadratic model, we found an orbital period Porb = 5.57062957(20) h and a Ṗorb value of 1.475(54)×10−10 s s−1. The addition of a cubic term to the model does not significantly improve the fit quality. We also determined a spin-period value of Pspin = 0.5915669(4) s and its first derivative Ṗspin = − 2.595(11) × 10−12 s s−1.

Conclusions. Our results confirm the scenario of a super-Eddington mass transfer rate; we also exclude a gravitational coupling between the orbit and the change in the oblateness of the companion star triggered by the nuclear luminosity of the companion star.
Simplified Rapid Protocol for Assessing the Thoracic Aortic Dimensions and Pathology with Noncontrast MR Angiography
Authors: Verma Megha , Yarlagadda Bharath , Hendrani Aditya , Bhat Ambarish P. , Kumar Senthil
Published: May 2019

Contrast enhanced magnetic resonance angiography (CE-MRA) is limited by long acquisition time and contrast exposure in aortic emergencies. To compare the effcacy of dark blood (DB) and bright blood (BB) noncontrast sequences with the gold standard CE-MRA using a novel protocol for performing consistent thoracic aortic measurements and thoracic aortic pathologies identifications. A total of 66 patients with suspected or known thoracic aortic pathology who underwent CE-MRA underwent DB and BB imaging prior to CE-MRA for planning purposes. Aortic dimension was measured at 10 standard reference points in the ascending, arch, and descending aorta. Detection of aortic pathologies was recorded individually for each noncontrast sequence. When comparing the CE-MRA to the DB images and CE-MRA to the BB images, a majority of the measurement differences were less than or equal to 2 mm or resulted in no change of diagnostic class (95% for CE-MRA vs. DB and 96% for CE-MRA vs. BB). Of the patients who had major changes in diagnostic class (e.g., changes in two or three classes), the absolute measurements were not clinically significant in any given patient to warrant a change in management. Individually, the DB and BB sequences allowed for accurate recognition of all 47 aortic pathologies. DB and BB sequences produced comparable and consistent measurements of the thoracic aorta when compared with CE-MRA. In a situation where CE-MRA is not readily available or contraindicated, noncontrast MRA using our protocol is a reliable alternative to CE-MRA for assessment of aortic pathologies.
Health Determinants of Asthma among Hispanic/Latino Children Enrolled in the Michigan Migrant and Seasonal Head Start Programs
Authors: Farabi Nabila , Song SuJin , Crockett Elahé , Song Won
Published: May 2019

Increasing prevalence of asthma in children in the United States is a major public health issue. Children in the Migrant and Seasonal Head Start (MSHS) program are one of the most vulnerable populations in the United States, with high rates of health disparities. We examined health determinants of asthma among Hispanic/Latino children enrolled in the Michigan MSHS programs. This study was a secondary data analysis based on the 2012 to 2013 ChildPlus dataset collected by Michigan Telamon Corporation. Sociodemographic and health information of 905 children aged 0 to 5 years was obtained from the dataset. Data were collected through interviews with parents by Telamon's specialists at each of the 18 Michigan MSHS centers. To determine children having asthma, health specialists at each center asked parents if their child/children had ever received asthma treatment. Weight status of children was categorized into nonoverweight/obese, overweight, and obese according to age- and sex-specific World Health Organization and Centers for Disease Control and Prevention growth chart standards. Multivariate logistic regression was used to identify asthma determinants. The overall prevalence of taking asthma treatment among Michigan MSHS children was 5.5%. Obese children had a higher odds ratio (OR) of asthma compared with nonoverweight/obese children (OR: 2.52; 95% confidence interval: 1.33–4.78). Children's age, health insurance status, and mothers' employment status were associated with asthma (p-values < 0.05). MSHS children are vulnerable to asthma, and their sociodemographic and obesity status are key determinants of having asthma. Identifying determinants of asthma might be helpful to design health policies and programs as well as implement health services for this population.
TLR1/2 ligand enhances antitumor efficacy of CTLA-4 blockade by increasing intratumoral Treg depletion
Authors: Sharma Naveen , Vacher Jean , Allison James P.
Published: May 2019

Significance

To overcome the challenge of nonresponsiveness or low effectiveness to current checkpoint blockade drugs, various combination therapies are under investigation for cancer treatment. In this study, we investigated a combination of Toll-like receptor 1/2 (TLR1/2) ligand and anti–CTLA-4 antibody in a mouse model of melanoma. TLR1/2 ligand enhanced the antitumor efficacy of anti–CTLA-4 by increasing Fcγ receptor IV expression, which in turn increased the depletion of tumor-infiltrating regulatory T cells. Whether ipilimumab causes Treg depletion in human patients is debatable; therefore, combining ipilimumab with Pam3CSK4 could lead to greater antitumor efficacy by introducing this modality. These findings are likely extensible to other checkpoint antibodies in cancer patients.
High-intensity focused ultrasound-induced mechanochemical transduction in synthetic elastomers
Authors: Kim Gun , Lau Vivian M. , Halmes Abigail J. , Oelze Michael L. , Moore Jeffrey S. , Li King C.
Published: May 2019

While study in the field of polymer mechanochemistry has yielded mechanophores that perform various chemical reactions in response to mechanical stimuli, there is not yet a triggering method compatible with biological systems. Applications such as using mechanoluminescence to generate localized photon flux in vivo for optogenetics would greatly benefit from such an approach. Here we introduce a method of triggering mechanophores by using high-intensity focused ultrasound (HIFU) as a remote energy source to drive the spatially and temporally resolved mechanical-to-chemical transduction of mechanoresponsive polymers. A HIFU setup capable of controlling the excitation pressure, spatial location, and duration of exposure is employed to activate mechanochemical reactions in a cross-linked elastomeric polymer in a noninvasive fashion. One reaction is the chromogenic isomerization of a naphthopyran mechanophore embedded in a polydimethylsiloxane (PDMS) network. Under HIFU irradiation evidence of the mechanochemical transduction is the observation of a reversible color change as expected for the isomerization. The elastomer exhibits this distinguishable color change at the focal spot, depending on ultrasonic exposure conditions. A second reaction is the demonstration that HIFU irradiation successfully triggers a luminescent dioxetane, resulting in localized generation of visible blue light at the focal spot. In contrast to conventional stimuli such as UV light, heat, and uniaxial compression/tension testing, HIFU irradiation provides spatiotemporal control of the mechanochemical activation through targeted but noninvasive ultrasonic energy deposition. Targeted, remote light generation is potentially useful in biomedical applications such as optogenetics where a light source is used to trigger a cellular response.
Criminal Thinking as a Risk Factor for Psychiatric Inpatient Aggression
Authors: Carr W. Amory , Rosenfeld Barry , Rotter Merrill
Published: May 2019

Thinking styles that predispose offenders to antisocial behavior have been shown to predict violence and aggression among inmates. This study explored this relationship among civil psychiatric inpatients. Medical records of N = 74 discharged patients were reviewed for inpatient incidents using the Overt Aggression Scale (OAS), occurring subsequent to the administration of several measures including the Psychological Inventory of Criminal Thinking Styles (PICTS), and Brief Psychiatric Rating Scale (BPRS). Univariate negative binomial regression models demonstrated that a higher rate of aggressive incidents was predicted by higher PICTS Denial of Harm, higher BPRS Hostile Suspiciousness scores, and lower educational attainment. Violence (i.e., physical aggression towards others) was predicted by higher BPRS Hostile Suspiciousness, lower education, and younger age in univariate analyses. In multivariate negative binomial regression models using the above independent predictors, higher BPRS-Hostile Suspiciousness scores and lower educational attainment significantly predicted both outcomes. This study’s results reinforce the importance of symptom-driven hostility to predicting inpatient aggression and violence, while highlighting the relatively minor role of specific criminal thinking styles in aggressive behavior among institutionalized psychiatric patients.
Ambient temperature influences metabolic substrate oxidation curves during running and cycling in healthy men
Authors: Gagnon Dominique D. , Perrier Lina , Dorman Sandra C. , Oddson Bruce , Larivière Céline , Serresse Olivier
Published: May 2019

Fat oxidation in cold environments and carbohydrate (CHO) use in hot environments are increased during exercise at steady‐state submaximal workloads. However, the influence of cold and heat on fat and CHO oxidation curves remain unknown. We therefore examined the influence of a cold and warm ambient temperature on fat and CHO oxidation across a wide range of exercise intensities during treadmill and cycle ergometer exercise. Nine, young, healthy, male subjects completed four trials, during which they performed an incremental peak oxygen consumption (⩒O2peak) test on a cycle ergometer or treadmill in a 4.6°C or 34.1°C environment. Substrate oxidation, maximal fat oxidation rate (MFO), and exercise intensity where MFO occurs (Fatmax) were assessed via indirect calorimetry. MFO was significantly greater in the cold vs. warm during the treadmill exercise (0.66 ± 0.31 vs. 0.43 ± 0.23 g min−1; p = 0.02) but not during cycling (0.45 ± 0.24 vs. 0.29 ± 0.11 g min−1; p = 0.076). MFO was also greater during treadmill vs. cycling exercise, irrespective of ambient temperature (0.57 g min−1 vs. 0.37 g min−1; p = 0.04). Fatmax was greater in the cold vs. warm for both treadmill (57 ± 20 vs. 37 ± 17%⩒O2peak; p = 0.025) and cycling (62 ± 28 vs. 36 ± 13%⩒O2peak; p = 0.003). Multiple, linear, mixed‐effects regressions revealed a strong influence of ambient temperature on substrate oxidation. We demonstrated that exercising in a cold environment increases MFO and Fatmax, predominantly during treadmill exercise. These results validate the implication of ambient temperature on energy metabolism over a wide range of exercise intensities.
How different is the evolution of sex-biased gene expression between plants and animals? A commentary on: ‘Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb’
Authors: Muyle Aline
Published: May 2019

This article comments on:

Guillaume G. Cossard, Melissa A. Toups and John R. Pannell. 2019. Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of Botany 123(7): 1119–1131.
Identifying and ranking potential driver genes of Alzheimer’s disease using multiview evidence aggregation
Authors: Mukherjee Sumit , Perumal Thanneer M , Daily Kenneth , Sieberts Solveig K , Omberg Larsson , Preuss Christoph , Carter Gregory W , Mangravite Lara M , Logsdon Benjamin A
Published: May 2019

Motivation

Late onset Alzheimer’s disease is currently a disease with no known effective treatment options. To better understand disease, new multi-omic data-sets have recently been generated with the goal of identifying molecular causes of disease. However, most analytic studies using these datasets focus on uni-modal analysis of the data. Here, we propose a data driven approach to integrate multiple data types and analytic outcomes to aggregate evidences to support the hypothesis that a gene is a genetic driver of the disease. The main algorithmic contributions of our article are: (i) a general machine learning framework to learn the key characteristics of a few known driver genes from multiple feature sets and identifying other potential driver genes which have similar feature representations, and (ii) A flexible ranking scheme with the ability to integrate external validation in the form of Genome Wide Association Study summary statistics. While we currently focus on demonstrating the effectiveness of the approach using different analytic outcomes from RNA-Seq studies, this method is easily generalizable to other data modalities and analysis types.

Results

We demonstrate the utility of our machine learning algorithm on two benchmark multiview datasets by significantly outperforming the baseline approaches in predicting missing labels. We then use the algorithm to predict and rank potential drivers of Alzheimer’s. We show that our ranked genes show a significant enrichment for single nucleotide polymorphisms associated with Alzheimer’s and are enriched in pathways that have been previously associated with the disease.

Availability and implementation

Source code and link to all feature sets is available at https://github.com/Sage-Bionetworks/EvidenceAggregatedDriverRanking.
ARMBIS: accurate and robust matching of brain image sequences from multiple modal imaging techniques
Authors: Shen Qi , Xiao Goayu , Zheng Yingwei , Wang Jie , Liu Yue , Zhu Xutao , Jia Fan , Su Peng , Nie Binbin , Xu Fuqiang , Zhang Bin
Published: May 2019

Motivation

Study of brain images of rodent animals is the most straightforward way to understand brain functions and neural basis of physiological functions. An important step in brain image analysis is to precisely assign signal labels to specified brain regions through matching brain images to standardized brain reference atlases. However, no significant effort has been made to match different types of brain images to atlas images due to influence of artifact operation during slice preparation, relatively low resolution of images and large structural variations in individual brains.

Results

In this study, we develop a novel image sequence matching procedure, termed accurate and robust matching brain image sequences (ARMBIS), to match brain image sequences to established atlas image sequences. First, for a given query image sequence a scaling factor is estimated to match a reference image sequence by a curve fitting algorithm based on geometric features. Then, the texture features as well as the scale and rotation invariant shape features are extracted, and a dynamic programming-based procedure is designed to select optimal image subsequences. Finally, a hierarchical decision approach is employed to find the best matched subsequence using regional textures. Our simulation studies show that ARMBIS is effective and robust to image deformations such as linear or non-linear scaling, 2D or 3D rotations, tissue tear and tissue loss. We demonstrate the superior performance of ARMBIS on three types of brain images including magnetic resonance imaging, mCherry with 4′,6-diamidino-2-phenylindole (DAPI) staining and green fluorescent protein without DAPI staining images.

Availability and implementation

The R software package is freely available at https://www.synapse.org/#!Synapse:syn18638510/wiki/591054 for Not-For-Profit Institutions. If you are a For-Profit Institution, please contact the corresponding author.

Supplementary information

Supplementary data are available at Bioinformatics online.
The epigenetic impacts of endocrine disruptors on female reproduction across generations†
Authors: Rattan Saniya , Flaws Jodi A
Published: May 2019

Humans and animals are repeatedly exposed to endocrine disruptors, many of which are ubiquitous in the environment. Endocrine disruptors interfere with hormone action; thus, causing non-monotonic dose responses that are atypical of standard toxicant exposures. The female reproductive system is particularly susceptible to the effects of endocrine disruptors. Likewise, exposures to endocrine disruptors during developmental periods are particularly concerning because programming during development can be adversely impacted by hormone level changes. Subsequently, developing reproductive tissues can be predisposed to diseases in adulthood and these diseases can be passed down to future generations. The mechanisms of action by which endocrine disruptors cause disease transmission to future generations are thought to include epigenetic modifications. This review highlights the effects of endocrine disruptors on the female reproductive system, with an emphasis on the multi- and transgenerational epigenetic effects of these exposures.
Genetics of human female infertility†
Authors: Yatsenko Svetlana A , Rajkovic Aleksandar
Published: May 2019

About 10% of women of reproductive age are unable to conceive or carry a pregnancy to term. Female factors alone account for at least 35% of all infertility cases and comprise a wide range of causes affecting ovarian development, maturation of oocytes, and fertilization competence, as well as the potential of a fertilized egg for preimplantation development, implantation, and fetal growth. Genetic abnormalities leading to infertility in females comprise large chromosome abnormalities, submicroscopic chromosome deletion and duplications, and DNA sequence variations in the genes that control numerous biological processes implicated in oogenesis, maintenance of ovarian reserve, hormonal signaling, and anatomical and functional development of female reproductive organs. Despite the great number of genes implicated in reproductive physiology by the study of animal models, only a subset of these genes is associated with human infertility. In this review, we mainly focus on genetic alterations identified in humans and summarize recent knowledge on the molecular pathways of oocyte development and maturation, the crucial role of maternal-effect factors during embryogenesis, and genetic conditions associated with ovarian dysgenesis, primary ovarian insufficiency, early embryonic lethality, and infertility.
Scientists' Warning on the Conservation of Subterranean Ecosystems
Authors: Mammola Stefano , Cardoso Pedro , Culver David C , Deharveng Louis , Ferreira Rodrigo L , Fišer Cene , Galassi Diana M P , Griebler Christian , Halse Stuart , Humphreys William F , Isaia Marco , Malard Florian , Martinez Alejandro , Moldovan Oana T , Niemiller Matthew L , Pavlek Martina , Reboleira Ana Sofia P S , Souza-Silva Marconi , Teeling Emma C , Wynne J Judson , Zagmajster Maja
Published: May 2019

In light of recent alarming trends in human population growth, climate change, and other environmental modifications, a “Warning to humanity” manifesto was published in BioScience in 2017. This call reiterated most of the ideas originally expressed by the Union of Concerned Scientists in 1992, including the fear that we are “pushing Earth's ecosystems beyond their capacities to support the web of life.” As subterranean biologists, we take this opportunity to emphasize the global importance and the conservation challenges associated with subterranean ecosystems. They likely represent the most widespread nonmarine environments on Earth, but specialized subterranean organisms remain among the least documented and studied. Largely overlooked in conservation policies, subterranean habitats play a critical role in the function of the web of life and provide important ecosystem services. We highlight the main threats to subterranean ecosystems and propose a set of effective actions to protect this globally important natural heritage.
Nakata index above 1500 mm2/m2 predicts death in absent pulmonary valve syndrome
Authors: Karaca-Altintas Yasemin , Laux Daniela , Gouton Marielle , Bensemlali Myriam , Roussin Régine , Hörer Jürgen , Raisky Olivier , Bonnet Damien
Published: May 2019

OBJECTIVES

Absent pulmonary valve syndrome is a rare congenital heart disease with severe airway compression due to dilatation of the pulmonary arteries (PAs). We investigated risk factors for death and prolonged mechanical ventilation (>7 days) and a threshold PA size for these outcomes.

METHODS

This retrospective 2-centre cohort study included 68 patients with complete repair between January 1996 and December 2015.

RESULTS

Median age at repair was 3.9 months (1.3–8.7 months), and median weight was 5 kg (4–7 kg). The mortality rate before hospital discharge was 12%, and the mortality rate at last follow-up was 19%. In multivariable analysis, risk factors for death were higher Nakata index [hazard ratio (HR) 1.001, 95% confidence interval (CI) 1.001–1.002; P < 0.001] and lower SpO2 (HR 1.06, 95% CI 1.02–1.09; P = 0.002). The accuracy of the Nakata index to predict death was excellent (area under the curve at 6 months: 0.92; P = 0.010). A Nakata index above 1500 mm2/m2 predicted mortality at 6 months with a sensitivity of 98% and a specificity of 82%. Twenty-five patients (37%) had prolonged mechanical ventilation. The only multivariable risk factor for prolonged ventilation was lower weight at repair (odds ratio 2.9, 95% CI 1.3–6.7; P = 0.008). Neither PA plasty nor the LeCompte manoeuvre had a protective effect on mortality or prolonged ventilation. A Nakata index above 1500 mm2/m2 remained a risk factor for mortality (P = 0.022) in patients who had a PA plasty or the LeCompte manoeuvre.

CONCLUSIONS

In patients with absent pulmonary valve syndrome, the Nakata index predicts mortality with a cut-off of 1500 mm2/m2. Lower weight at repair is the only multivariable risk factor for prolonged ventilation. Neither PA plasty nor the LeCompte manoeuvre had a protective effect on these outcomes.
The effectiveness of a professional development course: teachers’ perceptions
Authors: Sokel Frances
Published: May 2019

Although there has been increased interest in what constitutes effective professional development (PD) for in-service teachers in recent decades, the literature indicates that the issue continues to promote ongoing debate. Based upon the findings of previous research, this qualitative study set out to determine the extent to which, how, and why a PD course was considered effective in its contribution to the development and practice of the 28 in-service EFL teachers in Israel who participated in the course. Data from written reflective accounts, interviews, and field notes were collected and analysed. The findings identify various ways in which the course was considered effective, and reasons for such effectiveness, that, in turn, indicate the need for PD courses to be tailored to the current needs of practitioners as perceived by the course participants themselves.
Importance of EU regional support programmes for firm performance*
Authors: Beņkovskis Konstantīns , Tkačevs Oļegs , Yashiro Naomitsu
Published: May 2019

This paper investigates the effects of EU regional support on firm productivity, the number of employees and other performance indicators. We use a rich firm-level dataset for Latvia – the country, where investment activities are largely affected by the availability of EU funding. After controlling for the fact that more productive and larger firms are more likely to acquire EU finds, we find that participation in projects co-financed by the European Regional Development Fund (ERDF) increases firms’ employment, turnover and capital stock per employee immediately, while it raises their productivity only two years after the launch of the projects. ERDF beneficiaries that are initially less productive, larger, less capital intensive and more financially leveraged enjoy larger productivity gains.
Multimorbidity and the Transition Out of Full-Time Paid Employment: A Longitudinal Analysis of the Health and Retirement Study
Authors: van Zon Sander K R , Reijneveld Sijmen A , Galaurchi Anne , Mendes de Leon Carlos F , Almansa Josué , Bültmann Ute
Published: May 2019

Objectives

This study aims to examine whether older workers aged 50–64 years with multimorbidity are at increased risk to transition from full-time paid employment to part-time employment, partial retirement, unemployment, disability, economic inactivity, full retirement or die than workers without a chronic health condition and workers with one chronic health condition, and whether socioeconomic position (SEP) modifies these transitions.

Method

Using data from the Health and Retirement Study (1992–2014; n = 10,719), sub-distribution hazard ratios with 95% confidence intervals were calculated with a time-varying Fine and Gray competing-risks survival regression model to examine exit from full-time paid employment. We investigated the modifying effect of SEP by examining its interaction with multimorbidity.

Results

Workers with multimorbidity had a higher risk of transitioning to partial retirement (1.45; 1.22, 1.72), disability (1.84; 1.21, 2.78) and full retirement (1.63; 1.47, 1.81), and they had a higher mortality risk (2.58; 1.71, 3.88) than workers without chronic disorders. Compared to workers with one chronic health condition, workers with multimorbidity had an increased risk for partial (1.19; 1.02, 1.40) and full retirement (1.29; 1.17, 1.42), and mortality (1.49; 1.09, 2.04). Only SEP measured as educational level modified the relationship between multimorbidity and mortality.

Discussion

Workers with multimorbidity seem more prone to leave full-time paid employment than workers without or with one a chronic health condition. Personalized work accommodations may be necessary to help workers with multimorbidity prolong their working life.
Lipidomics in Ulcerative Colitis Reveal Alteration in Mucosal Lipid Composition Associated With the Disease State
Authors: Diab Joseph , Hansen Terkel , Goll Rasmus , Stenlund Hans , Ahnlund Maria , Jensen Einar , Moritz Thomas , Florholmen Jon , Forsdahl Guro
Published: May 2019

Background

The onset of ulcerative colitis (UC) is associated with alterations in lipid metabolism and a disruption of the balance between pro- and anti-inflammatory molecules. Only a few studies describe the mucosal lipid biosignatures during active UC. Moreover, the dynamics of lipid metabolism in the remission state is poorly defined. Therefore, this study aims to characterize mucosal lipid profiles in treatment-naïve UC patients and deep remission UC patients compared with healthy subjects.

Methods

Treatment-naïve UC patients (n = 21), UC patients in deep remission (n = 12), and healthy volunteers (n = 14) were recruited. The state of deep remission was defined by histological and immunological remission defined by a normalized TNF-α gene expression. Mucosa biopsies were collected by colonoscopy. Lipid analysis was performed by means of ultra-high performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS-MS). In total, 220 lipids from 11 lipid classes were identified.

Results

The relative concentration of 122 and 36 lipids was altered in UC treatment-naïve patients and UC remission patients, respectively, compared with healthy controls. The highest number of significant variations was in the phosphatidylcholine (PC), ceramide (Cer), and sphingomyelin (SM) composition. Multivariate analysis revealed discrimination among the study groups based on the lipid profile. Furthermore, changes in phosphatidylethanolamine(38:3), Cer(d18:1/24:0), and Cer(d18:1/24:2) were most distinctive between the groups.

Conclusion

This study revealed a discriminant mucosal lipid composition pattern between treatment-naïve UC patients, deep remission UC patients, and healthy controls. We report several distinctive lipids, which might be involved in the inflammatory response in UC, and could reflect the disease state.
Cmtm7 knockout inhibits B-1a cell development at the transitional (TrB-1a) stage
Authors: Liu Zhengyang , Liu Yuan , Li Ting , Wang Pingzhang , Mo Xiaoning , Lv Ping , Ge Qing , Ma Dalong , Han Wenling
Published: May 2019

Innate-like B-1a cells are an important cell population for production of natural IgM and interleukin-10 (IL-10), and act as the first line against pathogens. We determined that CMTM7 is essential for B-1a cell development. Following Cmtm7 (CKLF-like MARVEL transmembrane domain-containing 7) knockout, B-1a cell numbers decreased markedly in all investigated tissues. Using a bone marrow and fetal liver adoptive transfer model and conditional knockout mice, we showed that the reduction of B-1a cells resulted from B-cell-intrinsic defects. Because of B-1a cell loss, Cmtm7-deficient mice produced less IgM and IL-10, and were more susceptible to microbial sepsis. Self-renewal and homeostasis of mature B-1a cells in Cmtm7−/− mice were not impaired, suggesting the effect of Cmtm7 on B-1a cell development. Further investigations demonstrated that the function of Cmtm7 in B-1a cell development occurred at the specific transitional B-1a (TrB-1a) stage. Cmtm7 deficiency resulted in a slow proliferation and high cell death rate of TrB-1a cells. Thus, Cmtm7 controls B-1a cell development at the transitional stage.