bluuebunny/crossref_metadata_2025 huggingface dataset:
Unmasking the borderline coarctation: the utility of isoproterenol in the paediatric cardiac catheterisation laboratory
Authors: Patel Neil D. , Sullivan Patrick M. , Takao Cheryl M. , Badran Sarah , Ahdoot Joseph , Ing Frank F.
Published: March 2018

Background

One indication for intervention in coarctation of the aorta is a peak-to-peak gradient >20 mmHg. Gradients may be masked in patients under general anaesthesia and may be higher during exercise. Isoproterenol was given during cardiac catheterisation to simulate a more active physiologic state.

Objectives

We aimed to describe the haemodynamic effects of isoproterenol in patients with coarctation and the impact of intervention on the elicited gradients.

Methods

A retrospective study was performed on two-ventricle patients who underwent cardiac catheterisation for coarctation with isoproterenol testing.

Results

25 patients received isoproterenol before and after intervention. With isoproterenol, the mean diastolic (p=0.0015) and mean arterial (p=0.0065) blood pressures proximal to the coarctation decreased significantly. The mean systolic, diastolic, and mean arterial blood pressures distal to the coarctation decreased significantly (p<0.0001). In patients with a baseline gradient ⩽20 mmHg (n=17) at catheterisation, the median gradient increased from 10 (0–20) to 30 (15–50) mmHg (p<0.0001) with isoproterenol. Of these, 15 patients developed a gradient >20 mmHg. Post intervention, the median gradient decreased to 2 (0–29) mmHg, versus baseline, p=0.005, and with isoproterenol it decreased to 8 (0–27) mmHg, versus pre-intervention isoproterenol, p<0.0001. There were significant improvements in the gradients by Doppler (<0.0001) and by blood pressure cuff (p=0.0313). The gradients on isoproterenol best correlated with gradients by blood pressure cuff in the awake state (R2=0.76, p<0.0001).

Conclusions

Isoproterenol can be a useful tool to assess the significance of a coarctation and the effectiveness of an intervention. Percutaneous interventions can effectively reduce the gradients elicited by isoproterenol.
Assessment of the accuracy of nutrient calculations of five popular nutrition tracking applications
Authors: Griffiths Carly , Harnack Lisa , Pereira Mark A
Published: March 2018

Objective

To assess the accuracy of nutrient intake calculations from leading nutrition tracking applications (apps).

Design

Nutrient intake estimates from thirty 24 h dietary recalls collected using Nutrition Data System for Research (NDSR) were compared with intake calculations from these recalls entered by the researcher into five free nutrition tracking apps. Apps were selected from the Apple App Store based on consumer popularity from the list of free ‘Health and Fitness’ apps classified as a nutrition tracking apps.

Subjects

Dietary recall data collected from thirty lower-income adults.

Results

Correlations between nutrient intake calculations from NDSR and the nutrition tracking apps ranged from 0·73 to 0·96 for energy and macronutrients. Correlations for the other nutrients examined (Na, total sugars, fibre, cholesterol, saturated fat) ranged from 0·57 to 0·93. For each app, one or more mean nutrient intake calculations were significantly lower than those from NDSR. These differences included total protein (P=0·03), total fat (P=0·005), Na (P=0·02) and cholesterol (P=0·005) for MyFitnessPal; dietary fibre (P=0·04) for Fitbit; total protein (P=0·0004), total fat (P=0·008), Na (P=0·002), sugars (P=0·007), cholesterol (P=0·0006) and saturated fat (P=0·005) for Lose It!; Na (P=0·03) and dietary fibre (P=0·005) for MyPlate; and total fat (P=0·03) for Lifesum.

Conclusions

Findings suggest that nutrient calculations from leading nutrition tracking apps tend to be lower than those from NDSR, a dietary analysis software developed for research purposes. Further research is needed to evaluate the validity of the apps when foods consumed are entered by consumers.
TEM Morphometry Reveals Membrane Deficits in Parietal Cells Lacking Specific Ion Transporters
Authors: Miller ML , Gawenis LR , Andringa A , Shull GE
Published: March 2018

The late 1940s marked the appearance of the first publications using transmission electron microscopy (TEM) and by 1950, with improved embedding and sectioning methodology, reports began to include mammalian tissues (PubMed). However, 15 years lapsed before morphometry and stereology were integrated into TEM studies (Loud 1965; Elias 1971; Weibel 1969). The utility of a quantitative approach to electron microscopy was obvious, but its popularity has waxed and waned considerably over the last half century; its staunch supporters, however, have stayed the course (Weibel 2001; Diaspro 2004). Early computers, though slow and unreliable, brought some degree of automation to morphometry in the 1980s, but did little to ease tedium or increase accuracy (Caruntu 2002).
STEM Imaging of Lattice Fringes and beyond in a UHR In-Lens Field-Emission SEM
Authors: Van Ngo Vinh , Hernandez Mike , Roth Bill , Joy David C
Published: March 2018

The phase-contrast imaging of atomic lattices has now become commonplace for both Transmission Electron Microscopes (TEM) and Scanning Transmission Electron Microscopes (STEMs). Recently, however, bright-field STEM images of multi-wall carbon nanotubes (MWCNTs) recorded from an ultra-high resolution (UHR) in-lens field-emission scanning electron microscope (FE-SEM) operating at 30keV have also demonstrated lattice fringe resolution. One example of such an image containing multiple examples of fringe detail is shown in figure 1. The carbon lattice fringes were analyzed and their origin confirmed by the application of the FFT algorithms in the SMART image analysis program. The resulting power spectrum after thresholding to remove background noise (Figure 2) confirms that phase detail in the image extends down to about 5 Angstroms (0.5nm) and that well defined diffraction spots corresponding to a spacing of 3.4 Angstroms (0.34nm) generated by the (002) basal plane spacing of the graphite lattice are present.
Automated S/TEM Sample Preparation for Semiconductor Process Support
Authors: Cuti Greg , Jabbar Taha
Published: March 2018

The semiconductor industry has unquestionably entered the realm of nanotechnology. Critical dimensions of many features are specified in nanometers. Gate oxides are only a few nanometers thick. Barrier and seed layers for copper processes are not much more. Gate lengths are forecast at less than 20 nm by the end of the decade. Additionally, the drive to increase device density is leading to the adoption of FinFET and other new transistor designs that include complex three-dimensional structure. Even conventional planar CMOS designs now incorporate processes such as damascene interconnects that are inherently three dimensional. The combined need for higher spatial resolution and cross-sectional imaging of complex structures has led to a significant increase in the demand for scanning transmission electron microscopy (STEM) and (TEM) in semiconductor manufacturing operations.
A Novel Gemini® STEM Detector System
Authors: Vermeulen Jack , Jaksch Heiner
Published: March 2018

By using a scanning transmission electron microscopy (STEM) detector, the information limit for the Gemini® FESEMs can be extended beyond the nanometer range. A resolution of 0.8 nm at 30kV is now readily attainable and gives additional nanoscale information compared to conventional SEM detectors. The resolving power of the combined FESEM/STEM can be used to save processing time on TEM systems and enables high sample throughput for quality assurance applications and standard type measurements. The transmission mode of the FESEM has the advantages of avoiding chromatic aberration, allowing for a larger aperture so that higher transmission, signal-to-noise ratio and contrast enhancement due to the lower electron energy (10 - 30kV) can be obtained.
Microwave Protocols for Plant and Animal Paraffin Microtechnique
Authors: Schichnes Denise , Nemson Jeffrey A , Ruzin Steven E
Published: March 2018

The microwave oven is a valuable tool for light and electron microscopy microtechnique labs. Tissue processing times, traditionally taking up to two weeks, have been reduced to a few hours as a result of the implementation of microwave technology (Kok et al., 1988, Gibberson and Demaree, 2001). In addition, the quality of the tissue preparations has improved dramatically. Microwave ovens have also evolved since their first use in the laboratory. Early experiments were conducted using relatively crude commercial microwave ovens. Now, labs use microwave ovens with temperature probes, strict control over the magnetron (which generates the microwaves), variable power supplies, chamber cooling, and high microwave field uniformity.
Microscopy and Imaging of Foods — The Whys and Hows
Authors: Altan-Wojtas Paula
Published: March 2018

The use of microscopy and imaging methods to study foods is not a new idea. It has been going on since the first light microscopes were developed (White, 1970; White and Shenton, 1974-1984). Microscopy has been used to determine the quality, purity and safety of foodstuffs by detecting and identifying contaminants in foods. The short article by Stephen Carmichael in the May/June 2002 issue of Microscopy Today has again brought food microscopy into the spotlight. The article provided an opportunity to discuss present applications of food microscopy and to give some projections of where it is headed in the future. The reader may not realize that microscopy and imaging methods are used extensively by most major food companies worldwide for product development, quality control, and trouble shooting (Allan-Wojtas, 1999). Often, this work cannot be published because it contains proprietary information. The application of microscopy to food structure analysis is one of the best kept secrets in microscopy today.
The Scanning Confocal Electron Microscope
Authors: Zaluzec Nestor J
Published: March 2018

Imaging of sub-micron , sub-surface features of thick optically dense materials at high resolution has always been a difficult and/or time consuming task in materials research. For the most part this role has been relegated to technologically complex and expensive instrumentation having highly penetrating radiation, such as the synchrotron- based Scanning Transmission X-ray Microscope (STXM) or involves the careful preparation of thin cross-section slices for study using the Transmission/Scanning Transmission Electron Microscope (TEM/STEM).
Safe Handling of Embedding Media
Authors: Ellis E Ann
Published: March 2018

A previous article documented the health hazards associated with embedding media. This article will present specific measures that can be taken to diminish and/or eliminate problems when handling embedding media. Use of personal protective equipment is essential in all laboratory activities and especially when working with embedding media.
A Stable Lead Citrate Stain for Grids
Authors: Cohen-Gould Leona
Published: March 2018

For people in a small EM lab, keeping stable stain solutions that don't accumulate precipitates over time can be a problem. Over the last 26 years, I have adapted the method originally described by Venable and Coggeshall (1) to address this need
Color Metallography
Authors: Vander Voort George F
Published: March 2018

Color has historically seen limited use in metallography, mainly due to the cost of film and prints and the difficulty and cost of reproducing images in publications. However, with the growth of digital imaging, capturing color images is much simpler and cheaper. Also, printing images in color is inexpensive for in-house reports, and can be distributed cheaply on CDs, although reproduction in journals is still expensive. Color does have many advantages over black and white. First, the human eye is sensitive to only about forty shades of gray from white to black, but is sensitive to a vast number of colors. Tint etchants reveal features in the microstructure that often cannot be revealed using standard black and white etchants.
Automated, Robotic Preparation of Vitrified Samples for 2D and 3D Cryo Electron Microscopy
Authors: Frederik Peter M , Storms Marc MH
Published: March 2018

Fundamental research within the scope of cell and structural biology as well as nano-technology is increasingly focusing on unraveling interactive biological and biochemical processes and pathways at the macromolecular level. For this, high resolution transmission electron microscopy (TEM) is indispensable. Of paramount importance is the three-dimensional visualization of macromolecular structures and molecular machines in their native hydrated state. Their physical fixation within ultra-thin vitrified ice layers is the crucial starting point.
Mounting Media and Antifade Reagents
Authors: Collins Tony J
Published: March 2018

In the biomedical sciences, samples are mounted in a wide variety of media for examination by microscope. There are a wide variety of mounting media available with a correspondingly wide range of properties. Using the incorrect mounting medium may cause signal loss and optical aberrations; the correct mounting medium avoids such aberrations and preserves fluorescence signal with “anti-fading” properties. This article introduces mounting media for fluorescence microscopy, providing descriptions of their constituents and their properties, as well as accounts of users' experience

More detailed reviews of antifade reagents have been published by Ono et al. and Longin et al.. Papers describing the effect of refractive index (RI) mismatch have been published by Diaspro et al. and Hell et al..
Artifacts from Rapid Microwave Processing of Trematode Tissues (Ascocotyle pachycystisandleighi)
Authors: Armitage Mark H
Published: March 2018

The use of microwave energy to assist in the processing of biological tissues for microscopy has generated significant interest in recent years. Microwave (MW) processing has been used to prepare tissues for light microscopy (Carranza et al. 1990 [using parasite tissues]; van Dorp et al. 1995; Davis et al. 1997; Izumi et al 2000; and Rohr et al. 2001), as well as for electron microscopy (Kasa et al. 1982; Hopwood et al. 1984; Leong et al. 1985; Kang et al, 1991 [using parasite tissues]; Heumann 1992; Wagenaar et al. 1993; Login and Dvorak 1993; Giberson and Demaree 1995; Madden and Miriam 1997; Giberson et al. 1997; Morin et al. 1997; Petrali and Mills 1999; Massa and Arana-Chavez 2000; Hernandez and Guillen 2000 [using parasite tissues]; Demaree 2001; Giberson 2001).

Most reports, particularly those published by manufacturers of microwave ovens, have shown positive results regarding tissue ultrastructure, however discussion continues on possible mechanisms of preservation by the use of MW technology.
Precision Attachment of (Silica) Spheres to AFM Cantilever Tips
Authors: Huntington Shane , Nespolo Ms Sarah
Published: March 2018

Over the past decade the Atomic Force Microscope has been utilised in a myriad of applications across many fields of research and industry. One area that has been of particular interest is the measurement of small scale forces. The AFM is capable of measuring electrostatic and van der Waals forces with high precision based on small deflections of the AFM cantilever.

The forces between colloidal particles dominate the behaviour of a great variety of materials. The AFM has been extensively used to measure the forces between planar surfaces and individual colloid particles. One of the key driving forces for such experiments and the corresponding theoretical framework that has ensued is the ease of use of standard AFM tips for such measurements.
Marijuana Identification: A Test for Calcium in Cystolithic Hairs
Authors: Glattstein Baruch , Gorski Azriel
Published: March 2018

The identification of marijuana (Cannabis sativa) is a routine analysis in many forensic laboratories. An important part of this analysis is the identification of trichomes, commonly called cystolithic hairs, on plant particles. These hairs contain calcium carbonate, The very word cystolithic derives from this fact, coming from the Greek kustis and lithos meaning, “bag of stones”.

Trichomes are not unique to marijuana but are common on many species of plants. Thus, the mere presence of trichomes on a leaf surface is not sufficient. A required step in the identification of marijuana is the microscopical characterization of the cystoiithic hairs present on the leaf fragments.
Perfusion Fixation of Research Animals
Authors: Scouten Charles W , O'Connor Ryan , Cunningham Miles
Published: March 2018

Perfusion, washing out blood and using the open vascular channel to infuse fixative, is the standard first step of preparing animal tissues for later examination under a microscope. The rapid and homogeneous fixation resulting provides an advantage over immersion fixation that is usually used for biopsy and clinical tissue samples (Cammermeyer, 1960, Garman, 1990). A disadvantage is that brain tissue, and probably other soft tissues, prepared by perfusion has no retained extracellular space post perfusion, although living brain has about 20% extracellular space (discussed in Cragg, 1980). Perfused brain is also about 20% shrunk in whole organ volume from living brain size. The shrinkage is uneven, and distorts the relationships of structures. It is possible to avoid the organ shrinkage and distortion that follows a traditional perfusion, with little additional effort. This is a discussion of how to optimize your perfusion results, why the shrinkage occurs, and how it can be avoided.
New Fluorescent Labeling Technologies for Ultrasensitive Cytochemical and Histochemical Imaging
Authors: Johnson Iain
Published: March 2018

Immunofluorescence techniques using multicolor labeling and analysis of colocalization are essential for unraveling the structural and functional complexity of cells and tissues. Improvements in the capabilities of these techniques are dependent on the development of new fluorescent dyes and methods for attaching them to antibodies and other markers.

The Alexa Fluor® series of dyes developed by researchers at Molecular Probes, Inc. have optimized spectroscopic and physical properties that enable preparation of bioconjugates with consistently strong and photostable fluorescence output.
Penetration Rates of Formaldehyde
Authors: Hewlett Bryan R
Published: March 2018

Formaldehyde is one of the most rapidly penetrating fixatives used. Unfortunately, it is one of the slowest to fix tissue. This paradox was finally explained by Burnett in 1982. An fine description of the properties of formaldehyde may be found in John Kiernan's book.

The penetration rate of formaldehyde in mm/hr is a variable thing. It depends on how the data is obtained. It may also vary slightly depending on tissue type. The penetration rate of formaldehyde fixatives has been extensively studied, often with conflicting results. The penetration of non-coagulating fixatives is difficult to measure.
The Effect of Instrumental Uncertainties on AFM Indentation Measurements
Authors: VanLandingham Mark
Published: March 2018

The accuracy and precision of the quantitative measurements made with various types of scanning probe microscopes (SPMs) can be limited by instrumentation error. The piezoelectric scanners that are utilized in SPMs control either the motion of the cantilever probe with respect to a stationary sample or the motion of the sample with respect to a stationary probe. While these scanners offer many advantageous characteristics that are critical to the performance of SPMs, they also exhibit several behaviors, e.g., hysteresis and creep, that introduce uncertainties in measurements. Also, the nonlinearities associated with the photodiode used in the optical lever detection system can detract from the accuracy of measurements
Three Dimensional Imaging of Structure and Flow—Critical to Advances in Microfluidics
Authors: Hidrovo Carlos , Lundy Terence
Published: March 2018

Microfluidics, the study of fluid flow through structures with micrometer scale dimensions, is an increasingly important discipline within a number of commercial and industrial applications. One focus of active microfluidic research at the Stanford University Microscale Heat Transfer Laboratories (MHTL) is mass and heat transport in two-phase flows, which has applications in the cooling of integrated circuits and the management of water created in PEM fuel cells. At its core, two-phase microfluidics is the study of interactions between moving liquids and/or gases and/or solids (though not necessarily stationary) structures. Advanced confocal microscopy, with its ability to visualize and measure both flow and structure on a single instrumental platform, will certainly play a key role in the continuing development of microfluidic devices.
Is a Cs Corrector Necessary for Lorentz Vector Field Tomography?
Authors: Phatak Charudatta , De Graef Marc
Published: March 2018

Magnetic recording media based on patterned shapes are promising for applications in high density data storage. Optimizing the design of the patterned arrays requires characterization of the particle shapes and their relative locations, and the magnetostatic interactions between particles. To achieve this, one must determine the three dimensional (3D) magnetic induction in and around the nano magnets. We propose a method based on Vector Field Electron Tomography coupled with phase reconstructed Lorentz Microscopy to determine the 3D magnetic induction. This method can be broken down into two steps 1) Determination of the magnetic phase shift of the electron wave using phase reconstructed Lorentz microscopy and 2) Reconstruction (in 3D) of the magnetic induction in and around the magnetic particle using Vector Field Electron Tomography (VFET). First, we will discuss the theoretical development of VFET and then the importance of spherical aberration (Cs) correctors for Lorentz microscopy.
Optimizing Light Microscopy for Biological and Clinical Laboratories
Authors: Foster Barbara , Moss A G
Published: March 2018

Modern microscopy allows the life scientist to produce seductively beautiful images with powerful techniques developed by brilliant physical optical scientists, and yet be nearly completely confused with regard to the importance of the results. This is because modern microscopes are something like Lotus race cars: they have all the performance to fly in the hands of an experienced user, or crash and burn spectacularly in the hands of a novice. There is therefore great need for a comprehensive and accurate but accessible "drivers manual" for modern microscopical techniques.
Using a Formvar-Coated Bridge to Apply Formvar Support Film to TEM Grids
Authors: Shields John P
Published: March 2018

One conventional method for picking up ultrathin sections for transmission electron microscopy (TEM) is to prepare the mesh or slot grids with a formvar support film and then pick up your sections as they are floating in the knife boat. An alternative method is to first pick up sections on a naked grid and then lay them down on formvar film suspended over holes drilled in an aluminum bridge. I use this method when picking up serial sections on slot grids. A description of the method follows. The bridges I have were manufactured at the University of Georgia instrumentation Shop. They can also be purchased pre-made (for example, from SPI, Inc. They list them as Domino Racks), or one can make them from aluminum with a vise and drill. The sample bridge in the figure is similar to what I use. It is 5 cm long, 2.5 cm wide.
Days Can Be Converted To Hours, Minutes or Even Seconds When Using Microwave Technology in the Lab
Authors: Giberson Richard T , Demaree Richard S , Lee Steven B , Lee Michi
Published: March 2018

What happens when a cup of water and two ice cubes, contained in a bowl, are placed side by side in an 800 watt microwave oven and microwaved for two minutes at 100% power? The answer may not be obvious, even to the most ardent microwave user. The water will boil and the ice will remain essentially unmelted. This dichotomy of the results may appear puzzling to the casual observer, or may explain why your food does not defrost quite evenly. To the microwave, however, it all makes sense. Water is a dielectric and absorbs microwave energy. The net result is that it heats up. The ice under the above conditions is essentially transparent to the microwave and does not heat. It would take an ice wall greater than 30 meters thick (3.4 cm for 25° C water) to protect you from the microwave energy emitted by the standard household microwave, whereas a >170 nm thick piece of aluminum foil is all that is required to reflect that same energy.
The Particle Atlas Electronic Edition
Authors: Stewart Ian
Published: March 2018

In his preface to the first edition of The Particle Atlas, Jim Lodge talks of the challenge he posed to Dr. Walter McCrone in the 1950s to come up with a taxonomy for particles to assist in the identification of particles under the microscope. Jim's interest and the support of the Midwest Air Pollution Prevention Association and, laier, the US Public Health Service, gave birth to the first edition of The Particle Ailas. This first edition, published in 1967, was a single volume which combined guidance on particle separation and identification techniques with a collection of optical micrographs of reference particles. The demand for this reference work soon outpaced the supply. In the meantime, however, it had become obvious that reprinting was not the answer as increased application of the microscope, in all its implementations, to environmental pollution and industrial contamination had resulted in a need for a more comprehensive work.
Vascular Corrosion Casting Can Provide Quantitative as Well as Morphological Information on the Microvasculature of Organs and Tissues
Authors: Hossler Fred E
Published: March 2018

Complete casts of the vasculature of organs and tissues are obtained by infusing low viscosity resins into the vasculature and allowing the resin to polymerize. Dissolving away the surrounding tissue with alkali leaves a model of the intricate, three-dimensional distribution of vessels in that tissue, which is not easily obtainable by any other means, and which can then be studied with scanning electron microscopy (SEM), Because well prepared casts appear to faithfully replicate the true vascular anatomy of organs including the dimensions of vessels and details of imprints of the endothelial cells lining their lumens, they must also contain quantitative information about that vasculature.
Belief and Counterfactuality
Authors: Rafetseder Eva , Perner Josef
Published: March 2018

Abstract. The development and relation of counterfactual reasoning and false belief understanding were examined in 3- to 7-year-old children (N = 75) and adult controls (N = 14). The key question was whether false belief understanding engages counterfactual reasoning to infer what somebody else falsely believes. Findings revealed a strong correlation between false belief and counterfactual questions even in conditions in which children could commit errors other than the reality bias (rp = .51). The data suggest that mastery of belief attribution and counterfactual reasoning is not limited to one point in development but rather develops over a longer period. Moreover, the rare occurrence of reality errors calls into question whether young children’s errors in the classic false belief task are indeed the result of a failure to inhibit what they know to be actually the case. The data speak in favor of a teleological theory of belief attribution and challenges established theories of belief attribution.
Controlled drug delivery vehicles for cancer treatment and their performance
Authors: Senapati Sudipta , Mahanta Arun Kumar , Kumar Sunil , Maiti Pralay
Published: March 2018

Although conventional chemotherapy has been successful to some extent, the main drawbacks of chemotherapy are its poor bioavailability, high-dose requirements, adverse side effects, low therapeutic indices, development of multiple drug resistance, and non-specific targeting. The main aim in the development of drug delivery vehicles is to successfully address these delivery-related problems and carry drugs to the desired sites of therapeutic action while reducing adverse side effects. In this review, we will discuss the different types of materials used as delivery vehicles for chemotherapeutic agents and their structural characteristics that improve the therapeutic efficacy of their drugs and will describe recent scientific advances in the area of chemotherapy, emphasizing challenges in cancer treatments.
Automatic detection of image manipulations in the biomedical literature
Authors: Bucci Enrico M.
Published: March 2018

Images in scientific papers are used to support the experimental description and the discussion of the findings since several centuries. In the field of biomedical sciences, in particular, the use of images to depict laboratory results is widely diffused, at such a level that one would not err in saying that there is barely any experimental paper devoid of images to document the attained results. With the advent of software for digital image manipulation, however, even photographic reproductions of experimental results may be easily altered by researchers, leading to an increasingly high rate of scientific papers containing unreliable images. In this paper I introduce a software pipeline to detect some of the most diffuse misbehaviours, running two independent tests on a random set of papers and on the full publishing record of a single journal. The results obtained by these two tests support the feasibility of the software approach and imply an alarming level of image manipulation in the published record.
circHECTD1 promotes the silica-induced pulmonary endothelial–mesenchymal transition via HECTD1
Authors: Fang Shencun , Guo Huifang , Cheng Yusi , Zhou Zewei , Zhang Wei , Han Bing , Luo Wei , Wang Jing , Xie Weiping , Chao Jie
Published: March 2018

Excessive proliferation and migration of fibroblasts contribute to pulmonary fibrosis in silicosis, and both epithelial cells and endothelial cells participate in the accumulation of fibroblasts via the epithelial–mesenchymal transition (EMT) and the endothelial–mesenchymal transition (EndMT), respectively. A mouse endothelial cell line (MML1) was exposed to silicon dioxide (SiO2, 50 μg/cm2), and immunofluorescence and western blot analyses were performed to evaluate levels of specific endothelial and mesenchymal markers and to elucidate the mechanisms by which SiO2 induces the EndMT. Functional changes were evaluated by analyzing cell migration and proliferation. The mRNA and circular RNA (circRNA) levels were measured using qPCR and fluorescent in situ hybridization (FISH). Lung tissue samples from both Tie2-GFP mice exposed to SiO2 and silicosis patients were applied to confirm the observations from in vitro experiments. Based on the results from the current study, SiO2 increased the expression of mesenchymal markers (type I collagen (COL1A1), type III collagen (COL3A1) and alpha smooth muscle actin (α-SMA/Acta2)) and decreased the expression of endothelial markers (vascular endothelial cadherin (VE-Cad/Cdh 5) and platelet endothelial cell adhesion molecule-1 (PECAM1)), indicating the occurrence of the EndMT in response to SiO2 exposure both in vivo and in vitro. SiO2 concomitantly increased circHECTD1 expression, which, in turn, inhibited HECTD1 protein expression. SiO2-induced increases in cell proliferation, migration, and changes in marker levels were restored by either a small interfering RNA (siRNA) targeting circHECTD1 or overexpression of HECTD1 via the CRISPR/Cas9 system, confirming the involvement of the circHECTD1/HECTD1 pathway in the EndMT. Moreover, tissue samples from SiO2-exposed mice and silicosis patients confirmed the EndMT and change in HECTD1 expression. Our findings reveal a potentially new function for the circHECTD1/HECTD1 pathway and suggest a possible mechanism of fibrosis in patients with pulmonary silicosis.
TRIP13 promotes tumor growth and is associated with poor prognosis in colorectal cancer
Authors: Sheng Nengquan , Yan Li , Wu Kai , You Weiqiang , Gong Jianfeng , Hu Landian , Tan Gewen , Chen Hongqi , Wang Zhigang
Published: March 2018

Colorectal cancer (CRC) is one of the most common neoplasms worldwide. However, the mechanisms underlying its development are still poorly understood. Thyroid hormone Receptor Interactor 13 (TRIP13) is a key mitosis regulator, and recent evidence has shown that it is an oncogene. Here, we report that TRIP13, which is overexpressed in CRC, is correlated with the CEA (carcino-embryonic antigen), CA19-9 (carbohydrate antigen 19-9) and pTNM (pathologic primary tumor, lymph nodes, distant metastasis) classification. Multivariate analyses showed that TRIP13 might serve as an independent prognostic marker of CRC. We also found that TRIP13 promoted CRC cell proliferation, invasion and migration in vitro and subcutaneous tumor formation in vivo. Furthermore, the potential mechanism underlying these effects involves the interaction of TRIP13 with a 14-3-3 protein, YWHAZ, which mediates G2-M transition and epithelial-mesenchymal transition (EMT). Together, these findings suggest that TRIP13 may be a potential biomarker and therapeutic target for CRC.
Inhibition of p70 S6 kinase activity by A77 1726 induces autophagy and enhances the degradation of superoxide dismutase 1 (SOD1) protein aggregates
Authors: Sun Jing , Mu Yarong , Jiang Yuanyuan , Song Ruilong , Yi Jianxin , Zhou Jingsong , Sun Jun , Jiao Xinan , Prinz Richard A. , Li Yi , Xu Xiulong
Published: March 2018

Autophagy plays a central role in degrading misfolded proteins such as mutated superoxide dismutase 1 (SOD1), which forms aggregates in motor neurons and is involved in the pathogenesis of amyotrophic lateral sclerosis (ALS). Autophagy is activated when UNC-51-like kinase 1 (ULK1) is phosphorylated at S555 and activated by AMP-activated protein kinase (AMPK). Autophagy is suppressed when ULK1 is phosphorylated at S757 by the mechanistic target of rapamycin (mTOR). Whether p70 S6 kinase 1 (S6K1), a serine/threonine kinase downstream of mTOR, can also regulate autophagy remains uncertain. Here we report that inhibition of S6K1 by A77 1726, the active metabolite of an anti-inflammatory drug leflunomide, induced mTOR feedback activation and ULK1S757phosphorylation in NSC34 cells, a hybrid mouse motoneuron cell line. Unexpectedly, A77 1726 did not suppress but rather induced autophagy by increasing AMPKT172and ULK1S555phosphorylation. Similar observations were made with PF-4708671, a specific S6K1 inhibitor, or with S6K1 siRNA. Further studies showed that A77 1726 induced AMPK phosphorylation by activating the TGF-β-activated kinase 1 (TAK1). Functional studies revealed that A77 1726 induced co-localization of mutant SOD1G93Aprotein aggregates with autophagosomes and accelerated SOD1G93Aprotein degradation, which was blocked by inhibition of autophagy through autophagy-related protein 7 (ATG7) siRNA. Our study suggests that S6K1 inhibition induces autophagy through TAK1-mediated AMPK activation in NSC34 cells, and that blocking S6K1 activity by a small molecule inhibitor such as leflunomide may offer a new strategy for ALS treatment.
Myocardial Bmp2 gain causes ectopic EMT and promotes cardiomyocyte proliferation and immaturity
Authors: Prados Belén , Gómez-Apiñániz Paula , Papoutsi Tania , Luxán Guillermo , Zaffran Stephane , Pérez-Pomares José María , de la Pompa José Luis
Published: March 2018

During mammalian heart development, restricted myocardial Bmp2 expression is a key patterning signal for atrioventricular canal specification and the epithelial–mesenchyme transition that gives rise to the valves. Using a mouse transgenic line conditionally expressing Bmp2, we show that widespread Bmp2 expression in the myocardium leads to valve and chamber dysmorphogenesis and embryonic death by E15.5. Transgenic embryos show thickened valves, ventricular septal defect, enlarged trabeculae and dilated ventricles, with an endocardium able to undergo EMT both in vivo and in vitro. Gene profiling and marker analysis indicate that cellular proliferation is increased in transgenic embryos, whereas chamber maturation and patterning are impaired. Similarly, forced Bmp2 expression stimulates proliferation and blocks cardiomyocyte differentiation of embryoid bodies. These data show that widespread myocardial Bmp2 expression directs ectopic valve primordium formation and maintains ventricular myocardium and cardiac progenitors in a primitive, proliferative state, identifying the potential of Bmp2 in the expansion of immature cardiomyocytes.
Land use change and El Niño-Southern Oscillation drive decadal carbon balance shifts in Southeast Asia
Authors: Kondo Masayuki , Ichii Kazuhito , Patra Prabir K. , Canadell Joseph G. , Poulter Benjamin , Sitch Stephen , Calle Leonardo , Liu Yi Y. , van Dijk Albert I. J. M. , Saeki Tazu , Saigusa Nobuko , Friedlingstein Pierre , Arneth Almut , Harper Anna , Jain Atul K. , Kato Etsushi , Koven Charles , Li Fang , Pugh Thomas A. M. , Zaehle Sönke , Wiltshire Andy , Chevallier Frederic , Maki Takashi , Nakamura Takashi , Niwa Yosuke , Rödenbeck Christian
Published: March 2018

An integrated understanding of the biogeochemical consequences of climate extremes and land use changes is needed to constrain land-surface feedbacks to atmospheric CO2 from associated climate change. Past assessments of the global carbon balance have shown particularly high uncertainty in Southeast Asia. Here, we use a combination of model ensembles to show that intensified land use change made Southeast Asia a strong source of CO2 from the 1980s to 1990s, whereas the region was close to carbon neutral in the 2000s due to an enhanced CO2 fertilization effect and absence of moderate-to-strong El Niño events. Our findings suggest that despite ongoing deforestation, CO2 emissions were substantially decreased during the 2000s, largely owing to milder climate that restores photosynthetic capacity and suppresses peat and deforestation fire emissions. The occurrence of strong El Niño events after 2009 suggests that the region has returned to conditions of increased vulnerability of carbon stocks.
Memory effects can make the transmission capability of a communication channel uncomputable
Authors: Elkouss David , Pérez-García David
Published: March 2018

Most communication channels are subjected to noise. One of the goals of information theory is to add redundancy in the transmission of information so that the information is transmitted reliably and the amount of information transmitted through the channel is as large as possible. The maximum rate at which reliable transmission is possible is called the capacity. If the channel does not keep memory of its past, the capacity is given by a simple optimization problem and can be efficiently computed. The situation of channels with memory is less clear. Here we show that for channels with memory the capacity cannot be computed to within precision 1/5. Our result holds even if we consider one of the simplest families of such channels—information-stable finite state machine channels—restrict the input and output of the channel to 4 and 1 bit respectively and allow 6 bits of memory.
The human cortex possesses a reconfigurable dynamic network architecture that is disrupted in psychosis
Authors: Reinen Jenna M. , Chén Oliver Y. , Hutchison R. Matthew , Yeo B. T. Thomas , Anderson Kevin M. , Sabuncu Mert R. , Öngür Dost , Roffman Joshua L. , Smoller Jordan W. , Baker Justin T. , Holmes Avram J.
Published: March 2018

Higher-order cognition emerges through the flexible interactions of large-scale brain networks, an aspect of temporal coordination that may be impaired in psychosis. Here, we map the dynamic functional architecture of the cerebral cortex in healthy young adults, leveraging this atlas of transient network configurations (states), to identify state- and network-specific disruptions in patients with schizophrenia and psychotic bipolar disorder. We demonstrate that dynamic connectivity profiles are reliable within participants, and can act as a fingerprint, identifying specific individuals within a larger group. Patients with psychotic illness exhibit intermittent disruptions within cortical networks previously associated with the disease, and the individual connectivity profiles within specific brain states predict the presence of active psychotic symptoms. Taken together, these results provide evidence for a reconfigurable dynamic architecture in the general population and suggest that prior reports of network disruptions in psychosis may reflect symptom-relevant transient abnormalities, rather than a time-invariant global deficit.
Robustness of anthropogenically forced decadal precipitation changes projected for the 21st century
Authors: Zhang Honghai , Delworth Thomas L.
Published: March 2018

Precipitation is characterized by substantial natural variability, including on regional and decadal scales. This relatively large variability poses a grand challenge in assessing the significance of anthropogenically forced precipitation changes. Here we use multiple large ensembles of climate change experiments to evaluate whether, on regional scales, anthropogenic changes in decadal precipitation mean state are distinguishable. Here, distinguishable means the anthropogenic change is outside the range expected from natural variability. Relative to the 1950–1999 period, simulated anthropogenic shifts in precipitation mean state for the 2000–2009 period are already distinguishable over 36–41% of the globe—primarily in high latitudes, eastern subtropical oceans, and the tropics. Anthropogenic forcing in future medium-to-high emission scenarios is projected to cause distinguishable shifts over 68–75% of the globe by 2050 and 86–88% by 2100. Our findings imply anthropogenic shifts in decadal-mean precipitation will exceed the bounds of natural variability over most of the planet within several decades.
Automated generation and ensemble-learned matching of X-ray absorption spectra
Authors: Zheng Chen , Mathew Kiran , Chen Chi , Chen Yiming , Tang Hanmei , Dozier Alan , Kas Joshua J. , Vila Fernando D. , Rehr John J. , Piper Louis F. J. , Persson Kristin A. , Ong Shyue Ping
Published: March 2018

X-ray absorption spectroscopy (XAS) is a widely used materials characterization technique to determine oxidation states, coordination environment, and other local atomic structure information. Analysis of XAS relies on comparison of measured spectra to reliable reference spectra. However, existing databases of XAS spectra are highly limited both in terms of the number of reference spectra available as well as the breadth of chemistry coverage. In this work, we report the development of XASdb, a large database of computed reference XAS, and an Ensemble-Learned Spectra IdEntification (ELSIE) algorithm for the matching of spectra. XASdb currently hosts more than 800,000 K-edge X-ray absorption near-edge spectra (XANES) for over 40,000 materials from the open-science Materials Project database. We discuss a high-throughput automation framework for FEFF calculations, built on robust, rigorously benchmarked parameters. FEFF is a computer program uses a real-space Green’s function approach to calculate X-ray absorption spectra. We will demonstrate that the ELSIE algorithm, which combines 33 weak “learners” comprising a set of preprocessing steps and a similarity metric, can achieve up to 84.2% accuracy in identifying the correct oxidation state and coordination environment of a test set of 19 K-edge XANES spectra encompassing a diverse range of chemistries and crystal structures. The XASdb with the ELSIE algorithm has been integrated into a web application in the Materials Project, providing an important new public resource for the analysis of XAS to all materials researchers. Finally, the ELSIE algorithm itself has been made available as part of veidt, an open source machine-learning library for materials science.
An effective method to screen sodium-based layered materials for sodium ion batteries
Authors: Zhang Xu , Zhang Zihe , Yao Sai , Chen An , Zhao Xudong , Zhou Zhen
Published: March 2018

Due to the high cost and insufficient resource of lithium, sodium-ion batteries are widely investigated for large-scale applications. Typically, insertion-type materials possess better cyclic stability than alloy-type and conversion-type ones. Therefore, in this work, we proposed a facile and effective method to screen sodium-based layered materials based on Materials Project database as potential candidate insertion-type materials for sodium ion batteries. The obtained Na-based layered materials contains 38 kinds of space group, which reveals that the credibility of our screening approach would not be affected by the space group. Then, some important indexes of the representative materials, including the average voltage, volume change and sodium ion mobility, were further studied by means of density functional theory computations. Some materials with extremely low volume changes and Na diffusion barriers are promising candidates for sodium ion batteries. We believe that our classification algorithm could also be used to search for other alkali and multivalent ion-based layered materials, to accelerate the development of battery materials.
De Novo Design of Potent, Insecticidal Synthetic Mimics of the Spinosyn Macrolide Natural Products
Authors: Crouse Gary D. , Demeter David A. , Samaritoni Geno , McLeod Casandra L. , Sparks Thomas C.
Published: March 2018

New insect pest control agents are needed to meet the demands to feed an expanding global population, to address the desire for more environmentally-friendly insecticide tools, and to fill the loss of control options in some crop-pest complexes due to development of insecticide resistance. The spinosyns are a highly effective class of naturally occurring, fermentation derived insecticides, possessing a very favorable environmental profile. Chemically, the spinosyns are composed of a large complex macrolide tetracycle coupled to two sugars. As a means to further exploit this novel class of natural product-based insecticides, molecular modeling studies coupled with bioactivity-directed chemical modifications were used to define a less complex, synthetically accessible replacement for the spinosyn tetracycle. These studies lead to the discovery of highly insecticidal analogs, possessing a simple tri-aryl ring system as a replacement for the complex macrolide tetracycle.
Low Temperature-Mediated Enhancement of Photoacoustic Imaging Depth
Authors: Mahmoodkalayeh Sadreddin , Jooya Hossein Z. , Hariri Ali , Zhou Yang , Xu Qiuyun , Ansari Mohammad A. , Avanaki Mohammad R. N.
Published: March 2018

We study the temperature dependence of the underlying mechanisms related to the signal strength and imaging depth in photoacoustic imaging. The presented theoretical and experimental results indicate that imaging depth can be improved by lowering the temperature of the intermediate medium that the laser passes through to reach the imaging target. We discuss the temperature dependency of optical and acoustic properties of the intermediate medium and their changes due to cooling. We demonstrate that the SNR improvement of the photoacoustic signal is mainly due to the reduction of Grüneisen parameter of the intermediate medium which leads to a lower level of background noise. These findings may open new possibilities toward the application of biomedical laser refrigeration.