bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing the impact degree and areal degradation extent of the benthic ecosystem caused by different human activities.
Authors: Van Hoey Gert , De Backer Annelies , Hostens Kris
Published: March 2018

How sustainable are human activities and at what pace do they impact the ecosystem? An ongoing debate urging for uniform assessments. The EU Nature Directives (Marine Strategy Framework, Habitat and Water Framework Directives) provide good bases for scientifically sound assessments. However, they all have different assessment criteria, hampering the objective comparison of the impact degree and the areal extent of degradation caused by human activities. In this study, we applied a harmonized and uniform set of biodiversity indicators, as defined for MSFD-Descriptor 1 with respect to the benthic ecosystem in the Belgian North Sea. We assessed the impact of dredge disposal and aggregate extraction, two activities only allowed in dedicated zones, and compared this to the impact of the more widespread fishery activity. At certain pressure thresholds (e.g. volume disposed, volume and frequency of extraction, number of trawls), all activities caused a decrease in benthic habitat quality. However, for each activity the thresholds and the areal extent of degradation were quite different dependent on the benthic habitat type in which the activity took place. Such detailed insights on pressure footprints are necessary, to allow for an integrated evaluation of the biodiversity status across multiple activities within different marine regions.
Integrative, regional assessment of bottom trawling impact on benthic habitats in the east Atlantic.
Authors: Van Hoey Gert , Eigaard Ole Ritzau , Van Kooten Tobias , Valenko Sebastian , Rijnsdorp Adriaan
Published: March 2018

Based on a European union request, the International Council for the Exploration of the Sea (ICES) has explored and advised on indicators of pressure and impact of bottom trawling on the seabed, and of trade-offs in the catch and value of landings. Such assessment frameworks combine pressure (trawling intensity) with benthic habitats and their sensitivity to estimate the impacts on regional scale. The main differences between the indicators lay in their underlying scientific basis for determining sensitivity. Two approaches, the longevity and the population dynamic approach, are based on a statistical prediction of the longevity distribution of the benthic community, which is a practically very attractive way to capture sensitivity to trawling. The BH3 approach uses a categorical scoring approach for sensitivity. The BH2 relies on empirical observations to estimate changes in Margaleff diversity. In general, the use of continuous environmental variables, rather than the EUNIS habitat classes seemed promising for assessing impacts as they result in larger gradients in the sensitivity layer. Major steps forward in assessing the impact of bottom trawling were made, but improved parameterization and further ground-truthing is required, which will be further taken up in the ICES working group WGFBIT.
NuRD and CAF-1-mediated silencing of the D4Z4 array is modulated by DUX4-induced MBD3L proteins
Authors: Campbell Amy E , Shadle Sean C , Jagannathan Sujatha , Lim Jong-Won , Resnick Rebecca , Tawil Rabi , van der Maarel Silvère M , Tapscott Stephen J
Published: March 2018

The DUX4 transcription factor is encoded by a retrogene embedded in each unit of the D4Z4 macrosatellite repeat. DUX4 is normally expressed in the cleavage-stage embryo, whereas chromatin repression prevents DUX4 expression in most somatic tissues. Failure of this repression causes facioscapulohumeral muscular dystrophy (FSHD) due to mis-expression of DUX4 in skeletal muscle. In this study, we used CRISPR/Cas9 engineered chromatin immunoprecipitation (enChIP) locus-specific proteomics to characterize D4Z4-associated proteins. These and other approaches identified the Nucleosome Remodeling Deacetylase (NuRD) and Chromatin Assembly Factor 1 (CAF-1) complexes as necessary for DUX4 repression in human skeletal muscle cells and induced pluripotent stem (iPS) cells. Furthermore, DUX4-induced expression of MBD3L proteins partly relieved this repression in FSHD muscle cells. Together, these findings identify NuRD and CAF-1 as mediators of DUX4 chromatin repression and suggest a mechanism for the amplification of DUX4 expression in FSHD muscle cells.
Adult-born neurons facilitate olfactory bulb pattern separation during task engagement
Authors: Li Wankun L , Chu Monica W , Wu An , Suzuki Yusuke , Imayoshi Itaru , Komiyama Takaki
Published: March 2018

The rodent olfactory bulb incorporates thousands of newly generated inhibitory neurons daily throughout adulthood, but the role of adult neurogenesis in olfactory processing is not fully understood. Here we adopted a genetic method to inducibly suppress adult neurogenesis and investigated its effect on behavior and bulbar activity. Mice without young adult-born neurons (ABNs) showed normal ability in discriminating very different odorants but were impaired in fine discrimination. Furthermore, two-photon calcium imaging of mitral cells (MCs) revealed that the ensemble odor representations of similar odorants were more ambiguous in the ablation animals. This increased ambiguity was primarily due to a decrease in MC suppressive responses. Intriguingly, these deficits in MC encoding were only observed during task engagement but not passive exposure. Our results indicate that young olfactory ABNs are essential for the enhancement of MC pattern separation in a task engagement-dependent manner, potentially functioning as a gateway for top-down modulation.
Method for identification of condition-associated public antigen receptor sequences
Authors: Pogorelyy Mikhail V , Minervina Anastasia A , Chudakov Dmitriy M , Mamedov Ilgar Z , Lebedev Yuri B , Mora Thierry , Walczak Aleksandra M
Published: March 2018

Diverse repertoires of hypervariable immunoglobulin receptors (TCR and BCR) recognize antigens in the adaptive immune system. The development of immunoglobulin receptor repertoire sequencing methods makes it possible to perform repertoire-wide disease association studies of antigen receptor sequences. We developed a statistical framework for associating receptors to disease from only a small cohort of patients, with no need for a control cohort. Our method successfully identifies previously validated Cytomegalovirus and type one diabetes responsive TCRβ sequences .
A genome-wide investigation of microsatellite mismatches and the association with body mass among bird species
Authors: Fan Haiying , Guo Weibin
Published: March 2018

Mutation rate is usually found to covary with many life history traits of animals such as body mass, which has been readily explained by the higher number of mutation opportunities per unit time. Although the precise reason for the pattern is not yet clear, to determine the universality of this pattern, we tested whether life history traits impact another form of genetic mutation, the motif mismatches in microsatellites. Employing published genome sequences from 65 avian species, we explored the motif mismatches patterns of microsatellites in birds on a genomic level and assessed the relationship between motif mismatches and body mass in a phylogenetic context. We found that small-bodied species have a higher average mismatches and we suggested that higher heterozygosity in imperfect microsatellites lead to the increase of motif mismatches. Our results obtained from this study imply that a negative body mass trend in mutation rate may be a general pattern of avian molecular evolution.
A Progress Report on Efforts to Address Lead by Public School Districts
Authors: Sanborn Lily H. , Carpenter Adam T.
Published: March 2018

Media reports in 2016 brought lead contamination of drinking water to public attention, particularly at schools where young students can be exposed to lead by drinking at contaminated outlets. In an effort to assess nationwide progress on addressing this potential health risk, this study sought to determine the status of lead testing, remediation, and long‐term management strategies in public school districts serving the nation's 15 most populous urbanized areas. Data were collected from publicly available information and through direct interaction with school districts. All districts under consideration have implemented some form of US Environmental Protection Agency‐recommended lead testing program, and districts with elevated lead levels have performed corrective actions including flushing, outlet repairs/replacement, and filtration. This study outlines districts' testing programs, approaches to lead‐management, plans for continued monitoring, communication strategies, and self‐assessed successes and challenges.
Synthesis and Structural Characterization of Non‐Homoleptic Carbamato Complexes of VV and WVI and Their Facile Implantation onto Silica Surfaces
Authors: Bresciani Giulio , Bortoluzzi Marco , Zacchini Stefano , Gabbani Alessio , Pineider Francesco , Marchetti Fabio , Pampaloni Guido
Published: March 2018

The vanadium(V) amido‐carbamato derivatives VO(NR2)(O2CNR2)2 (R = Me, 1; Et, 2) are obtained by the reaction of VOCl3 with preformed carbamato species (ammonium or sodium carbamates). The synthesis of an ionic ammonium chlorido‐amide of WVI, 3, is performed using WOCl4 and diethylamine as precursors. Moreover, the reactivity of 3 with CO2 is investigated. Mixed WVI chlorido‐carbamato compounds, 4 and 5, are obtained by the reaction of WOCl4 with stoichiometric amounts of sodium diethylcarbamate. All of the products are characterized by analytical and spectroscopic methods (IR spectroscopy, multinuclear NMR spectroscopy) and by X‐ray diffraction in the cases of 3 and 4. DFT calculations are useful to elucidate the structures of the compounds and to give insight into the various reaction pathways. The combination of 2 or 5 with amorphous silica gives solid materials, which are characterized by inductively coupled plasma‐optical emission spectroscopy (ICP‐OES) and energy dispersive X‐ray spectroscopy (EDS) coupled to scanning electron microscopy (SEM).
Multiple strategies to identify HIV‐positive black men who have sex with men and transgender women in New York City: a cross‐sectional analysis of recruitment results
Authors: Franks Julie , Mannheimer Sharon B , Hirsch‐Moverman Yael , Hayes‐Larson Eleanor , Colson Paul W , Ortega Hugo , El‐Sadr Wafaa M
Published: March 2018

Introduction

Black men who have sex with men and transgender women are at high risk for HIV infection, but are more likely to be unaware of their infection or not in care for diagnosed HIV compared to other races. Respondent driven sampling has been advanced as a method to reach stigmatized and hidden populations for HIV testing. We compared strategies to recruit black, substance‐using men who have sex with men and transgender women to identify newly diagnosed HIV infection, or those previously diagnosed but not in care.

Methods

The STAR (Seek, Test, and Retain) study (ClinicalTrials.gov NCT01790360) used several recruitment strategies to identify black, substance‐using men who have sex with men and transgender women with undiagnosed HIV infection or with previously diagnosed HIV infection but who were not in HIV care. Respondent‐driven sampling, community‐based recruitment and online advertising were used to recruit participants. Incentivized peer referral was integrated into all recruitment strategies. Participants completed interviewer‐administered questionnaires and HIV testing. Demographic and HIV risk‐related characteristics and recruitment strategy were summarized and stratified by HIV status. Associations were tested using Pearson's chi‐squared, Fisher's exact, and Wilcoxon rank sum tests. Factors associated with HIV‐positive diagnosis at p < 0.1 were included in a multivariable logistic regression model.

Results

From July 2012 through October 2015, the study enrolled 1929 participants; 96.3% men who have sex with men and 3.7% transgender women. Behavioural risk factors included recent condomless anal sex (55.6%) and recent substance use during sex (73.1%). HIV prevalence was 8.7%. In multivariable analysis, significant associations with HIV infection included being transgender; non‐Hispanic black; gay/homosexual orientation; not homeless; and less likely to have insufficient income for necessities. Among recruitment strategies, respondent driven sampling was least effective in identifying HIV‐positive participants.

Conclusions

Integrating multiple recruitment strategies yielded a large sample of black men who have sex with men and transgender women at substantial risk for HIV. Respondent‐driven sampling was less effective than other strategies at identifying men who have sex with men and transgender women with HIV.
The CP-violating 2HDM in light of a strong first order electroweak phase transition and implications for Higgs pair production
Authors: Basler P. , Mühlleitner M. , Wittbrodt J.
Published: March 2018

Abstract

We investigate the strength of the electroweak phase transition (EWPT) within the CP-violating 2-Higgs-Doublet Model (C2HDM). The 2HDM is a simple and well-studied model, which can feature CP violation at tree level in its extended scalar sector. This makes it, in contrast to the Standard Model (SM), a promising candidate for explaining the baryon asymmetry of the universe through electroweak baryogenesis. We apply a renormalisation scheme which allows efficient scans of the C2HDM parameter space by using the loop-corrected masses and mixing matrix as input parameters. This procedure enables us to investigate the possibility of a strong first order EWPT required for baryogenesis and study its phenomenological implications for the LHC. Like in the CP-conserving (real) 2HDM (R2HDM) we find that a strong EWPT favours mass gaps between the non-SM-like Higgs bosons. These lead to prominent final states comprised of gauge+Higgs bosons or pairs of Higgs bosons. In contrast to the R2HDM, the CP-mixing of the C2HDM also favours approximately mass degenerate spectra with dominant decays into SM particles. The requirement of a strong EWPT further allows us to distinguish the C2HDM from the R2HDM using the signal strengths of the SM-like Higgs boson. We additionally find that a strong EWPT requires an enhancement of the SM-like trilinear Higgs coupling at next-to-leading order (NLO) by up to a factor of 2.4 compared to the NLO SM coupling, establishing another link between cosmology and collider phenomenology. We provide several C2HDM benchmark scenarios compatible with a strong EWPT and all experimental and theoretical constraints. We include the dominant branching ratios of the non-SM-like Higgs bosons as well as the Higgs pair production cross section of the SM-like Higgs boson for every benchmark point. The pair production cross sections can be substantially enhanced compared to the SM and could be observable at the high-luminosity LHC, allowing access to the trilinear Higgs couplings.
Gravitational parity anomaly with and without boundaries
Authors: Kurkov Maxim , Vassilevich Dmitri
Published: March 2018

Abstract

In this paper we consider gravitational parity anomaly in three and four dimensions. We start with a re-computation of this anomaly on a 3D manifold without boundaries and with a critical comparison of our results to the previous calculations. Then we compute the anomaly on 4D manifolds with boundaries with local bag boundary conditions. We find, that gravitational parity anomaly is localized on the boundary and contains a gravitational Chern-Simons terms together with a term depending of the extrinsic curvature. We also discuss the main properties of the anomaly, as the conformal invariance, relations between 3D and 4D anomalies, etc.
Is Partial or Total Thyroidectomy Associated with Risk of Long‐Term Osteoporosis: A Nationwide Population‐Based Study
Authors: Hung Chien‐Ling , Yeh Chih‐Ching , Sung Pi‐Shan , Hung Chung‐Jye , Muo Chih‐Hsin , Sung Fung‐Chang , Jou I‐Ming , Tsai Kuen‐Jer
Published: March 2018

Background

Whether thyroidectomy contributes to osteoporosis (OP) and osteoporotic fracture (OF) is a subject of debate. This study aimed to determine the effect of thyroidectomy on the risk of OP and OF.

Methods

This retrospective cohort study is based on patient data between January 2000 to December 2005 from the National Health Insurance Research Database. Patients who underwent thyroidectomy were enrolled in the thyroidectomy cohort, and the control cohort was selected by propensity score matching at a ratio of 1:4. Incident OP and OF cases were identified until the end of 2013. The thyroidectomy cohort to control cohort adjusted hazard ratio (aHR) for OP/OF was assessed through multivariable Cox proportional hazard regression analysis.

Results

Totals of 1426 and 5704 patients were included in the thyroidectomy and control cohorts, respectively. The incidence density of OP was higher in the thyroidectomy cohort (7.91/1000 person‐years) than in the control cohort (5.98/1000 person‐years), with an aHR of 1.43 (95% CI 1.16–1.77, p < 0.05). Younger patients, women, and patients with comorbidities were at a higher risk. The risks of postoperative OP/OF were significantly increased in patients who received thyroxine treatment for more than 1 year, both in the partial thyroidectomy group and in the total and subtotal thyroidectomy group (aHR: 2.47, 95% CI: 1.42–2.31 vs. aHR: 1.84, 95% CI: 1.22–2.76).

Conclusion

Thyroidectomy significantly increased the long‐term risk of OP. Younger patients, women, patients with comorbidities, and patients receiving chronic thyroxin treatment should be monitored for changes in postoperative bone density.
Computer‐based evaluation of Alzheimer's disease and mild cognitive impairment patients during a picture description task
Authors: Hernández‐Domínguez Laura , Ratté Sylvie , Sierra‐Martínez Gerardo , Roche‐Bergua Andrés
Published: March 2018

Introduction

We present a methodology to automatically evaluate the performance of patients during picture description tasks.

Methods

Transcriptions and audio recordings of the Cookie Theft picture description task were used. With 25 healthy elderly control (HC) samples and an information coverage measure, we automatically generated a population‐specific referent. We then assessed 517 transcriptions (257 Alzheimer's disease [AD], 217 HC, and 43 mild cognitively impaired samples) according to their informativeness and pertinence against this referent. We extracted linguistic and phonetic metrics which previous literature correlated to early‐stage AD. We trained two learners to distinguish HCs from cognitively impaired individuals.

Results

Our measures significantly (P < .001) correlated with the severity of the cognitive impairment and the Mini–Mental State Examination score. The classification sensitivity was 81% (area under the curve of receiver operating characteristics = 0.79) and 85% (area under the curve of receiver operating characteristics = 0.76) between HCs and AD and between HCs and AD and mild cognitively impaired, respectively.

Discussion

An automated assessment of a picture description task could assist clinicians in the detection of early signs of cognitive impairment and AD.
Middle Ordovician actinocerid nautiloids (Cephalopoda) from Xainza County, Tibet, western China, and their paleogeographic implications
Authors: Fang Xiang , Chen Tingen , Burrett Clive , Wang Yongsheng , Qu Yonggui , Zheng Chunzi , Zhang Yunbai , Zhang Yuandong , Li Wenjie
Published: March 2018

Actinocerid nautiloids from the Lhasai Formation in the Xainza region are studied systematically for the first time. The nautiloids are identified as Middle Ordovician in age based on stratigraphic correlations with those from North China, Sibumasu, North Australia (northern Gondwana), and North America (Laurentia). A cluster analysis shows strong affinities between the actinocerid nautiloids of the Lhasa Terrane and those of the Himalaya, North China, and Sibumasu terranes. Our results support Middle Ordovician paleogeographic reconstructions that place North China rather than South China much closer to Australia. Nine species assigned to six genera of Meitanoceratidae, Wutinoceratidae, Armenoceratidae, Ormoceratidae, and Discoactinoceratidae are described in detail:Pomphoceras nyalamense(Chen, 1975),Pomphoceras yaliense(Chen, 1975),Wutinocerascf.W.foerstei(Endo, 1930),Mesowutinoceras giganteumChen in Chen and Zou, 1984,Armenoceras tani(Grabau, 1922),Armenoceras teichertiEndo, 1932,Armenoceras xizangensenew species,Deiroceras globosomZou and Shen in Chen and Zou, 1984, andDiscoactinocerascf.D.multiplexumKobayashi, 1927.

UUID:http://zoobank.org/ba851fea-e107-4754-a0f4-a70744e325ab
A Statistical Treatment of the Stellar Rotational Velocities Which Considers the Break-Up Limit
Authors: Bernacca P. L.
Published: March 2018

This paper develops a new statistical approach to the study of the axial rotational velocities of the stars, by considering the break-up limit or any upper limit for the equatorial rotational velocities. The main conclusions are as follows: (1) For random orientation of the axis of rotation, the frequency function of the inclinationαto the line of sight is not sina, as assumed until now. (2) For stars with the same break-up velocityvb, the distribution ofαis given by :

wheref(y) is the distribution of the apparent velocitiesy=vsin α,vbeing the true rotational velocity. New integral equations governing the frequency function of α,yandvhave been derived and the correct procedure to treat observations has been discussed; a simple method is also suggested to get an approximate trend of the distribution of the true velocities directly from the observed histogram. The method of analysis proposed in this paper has been applied to a re-discussion of the rotational behaviour of a group of Be stars.
Changing invaders: trends of gigantism in insular introduced rats
Authors: VAN DER GEER ALEXANDRA A.E.
Published: March 2018

The degree and direction of morphological change in invasive species with a long history of introduction are insufficiently known for a larger scale than the archipelago or island group. Here, I analyse data for 105 island populations of Polynesian rats,Rattus exulans, covering the entirety of Oceania and Wallacea to test whether body size differs in insular populations and, if so, what biotic and abiotic features are correlated with it. All insular populations of this rat, except one, exhibit body sizes up to twice the size of their mainland conspecifics. Body size of insular populations is positively correlated with latitude, consistent with thermoregulatory predictions based on Bergmann's rule. Body size is negatively correlated with number of co-occurring mammalian species, confirming an ecological hypothesis of the island rule. The largest rats are found in the temperate zone of New Zealand, as well as on mammalian species-poor islands of Polynesia and the Solomon Islands. Carnivory in the form of predation on nesting seabird colonies seems to promote 1.4- to 1.9-fold body size increases.
Active Optics Improve Microscope’s Field of View
Authors: Potsaid Benjamin , Wen John T
Published: March 2018

Since the earliest explorations of the microscopic world in the 17th century and continuing to the present day, microscopists have continuously faced a challenge in that there is an inherent tradeoff between the resolution of the microscope and the size of the field of view--as the resolution of the microscope is increased to resolve smaller features, the observable area of the specimen decreases proportionally. While being a long recognized characteristic of the traditional microscope design, this tradeoff is becoming a significant hindrance as optical microscopes are being used in automated systems for advanced biotech research, medical diagnostics, robotic micromanipulation, and industrial inspection.
Infrared Chemical Imaging: Semi-Quantitative Analysis of Components
Authors: Tarr Jonathan , Nishikida Koichi , Izzia Federico
Published: March 2018

With new image analysis software for infrared spectroscopy, semi-quantitative studies can be performed without the use of standards providing rapid measurements of component concentrations when an approximate value is suitable or when quantitative standards are not available. Infrared spectroscopy has been used for many years to identify the composition of organic and other materials. Single or multi-component samples can be analyzed and their chemical structures determined by comparing their absorbance peaks to known spectral libraries or fundamental molecular transitions. This technique is used throughout the scientific community and provides rich information.
Water — A Clean “Glue” to Attach Hydrophilic Plates to an AFM Sample Stage
Authors: Gan Yang
Published: March 2018

Attaching a sample to the instrument's sample stage is commonly the first step in the operation of an AFM. For our commercial Digital Instruments Multimode AFM, a sample is usually attached to a magnetic sample puck by double-sided tape, the sample puck is then placed on the instrument’s magnetic sample stage, and analysis can begin.

The use of double-sided tape, however, has unpleasant consequences. First, the surface of the sample puck becomes quite sticky due to residual glue from the double-sided tape ! removing the sticky glue is not a happy job. One cannot just throw a soiled sample puck away! Second, double-sided tape does not always give satisfactory mechanical stability during AFM operation, especially when high resolution imaging is being carried out. Sometimes the tape-mounted sample will creep slowly, which can cause significant drift of AFM images. This is because the tapes and their adhesive films are made of pressure sensitive materials that tend to change shape when pressure and/or temperature vary.
Dissolving Osmium Tetroxide the Easy Way
Authors: Sherman Debby
Published: March 2018

Osmium crystals tend to cling to the glass ampoule walls making dissolving them difficult. Smashing the vials results in glass shards that may get into sample vials and can be dangerous, or carry into embedding media and damage diamond knives.

A simple trick to eliminate smashing osmium vials is to dip the sealed ampoule into liquid nitrogen. This releases the osmium crystals from the glass walls. Then simply break the vial using an ampoule cracker (available through EM supply houses) and pour the osmium crystals into a bottle containing the water for the OsO4 solution. Wait a few minutes to let the ampoule warm-up, and it is easy to see if all of the crystals have been dumped out of the ampoule. Let the solution sit overnight at room temperature in a hood and the next day the crystals will be totally dissolved.
Calibration Of Electron Microscopes: How To Do This, How Often, Pit-falls And Problems. M&M 2001 Experts' Session on Core Facility Management
Authors: Sherman Debby
Published: March 2018

This article is the third of a series transcribed from the discussion taped during the Core Facility Management session. Buileted paragraphs indicate comments by individuals attending the session.

D. Sherman: The next topic we are going to deal with has to do with calibration of electron microscopes. This became very important in my situation because we started dealing with people with nanotubes and nanovesicles and with very small things where they needed to have accurate size both in the SEM and the TEM magnification range. My own frustrations dealing with calibration, especially in the in between magnification, spurred me on to ask a couple of experts to give us some insight on what we should be doing with calibration - the problems associated with this and some general information about how to go about doing this in our standard facilities where money is short.
Scanning Impedance Microscopy: From Impedance Spectra to Impedance Images
Authors: Kalinin Sergei V , Bonnell Dawn A
Published: March 2018

The properties and performance of electronic devices are crucially dependent on interface-related phenomena. The presence of interfaces can enable electronic device functionality (p-n diodes, solar cells); alternatively, non-functional interfaces can degrade device performance (ohmic vs. non-ohmic contacts). The most versatile tools for semiconductor interface characterization are ac (impedance spectroscopy, C-V) and dc (I-V) transport measurements. However, due to the lack of spatial resolution, these methods often cannot separate the contributions from electroactive interfaces and contacts. This is especially true for the non-traditional electronic materials such as semiconductive oxides, nitrides, conductive polymers, etc. Combined with the tendency towards miniaturization of electronic devices, this clearly necessitates spatially resolved ac and dc transport measurements.
Alphabet Soup
Authors: Revel Jean Paul
Published: March 2018

I have just attended the 50th anniversary of EMSA in Boston, and what a grand show it was! Appropriately enough the organizers had brought together an impressive number of the pioneers in microscopy, and Sterling Newberry even prepared a book describing the early days of electron microscopy and a video in which said pioneers reminisce about how things were.
Specimen Capsules For Critical-Point Drying
Authors: Sepsenwol Sol
Published: March 2018

Since we do a lot of small-sample critical-point drying (CPD) for SEM, we assemble our own drying capsules which can be manufactured easily in quantity. Materials' cost at current prices is about $10 for 50 capsules. About 25 capsules can be manufactured in an hour. The completed capsule consists of a small polypropylene chamber with fine-mesh, stainless-steel screen caps at each end that allow easy exchange of solvents. shows the steps ofthe assembly process. The base of one capsule is cut off with a razor blade, the cap of a second capsule, for a bottom (Figure 1a). Chamber length can be 5 to 14mm. One-quarter-inch holes are punched through the center of each cap using a paper punch whose spring/detente has been removed to pass the caps' rim (Figure 1b). A sheet-metal shim punch is used to create 3/8" disks of 60-mesh stainless steel wire cloth.
A Novel Technique of Hair Removal to Examine the Cuticle of Arthropods
Authors: Philip Benjamin N , Shillington Cara
Published: March 2018

The highly structured arthropod cuticle is often adorned with dense hairs that conceal the underlying landscape. Thus, to examine the structures and patterns on the cuticle the overlying hairs must be removed with minimal damage to the cuticle itself. Different methods can be employed to eliminate hairs but the difficulty of this task is compounded by the small size and fragility of the exoskeleton to which the hairs are attached. If the hairs are removed using razor blades or scissors, not only is the debris from the cut hairs and the stubble from the remainder of the shaft left behind, but the cuticle is often broken in the course of gripping the exoskeleton. We developed a unique technique that cleanly removes hairs without leaving debris or damaging the structure. This technique has been successfully used to examine the cuticular surfaces of arthropods of varying sizes including spiders, bees, beetles and moths.
Improving Membrane Staining of Cultured Cells Using Ferrocyanide as a Post-Fixative
Authors: Nizet Stéphane
Published: March 2018

Lack of contrast is a common problem encountered when doing TEM of cultured cells, especially of membranes. Using ferrocyanide as a post-fixative can greatly improve membrane fixation and staining. This protocol has been used to study Caco-2 cells grown on PET membranes (the “Caco model”). Caco-2 is a colon cancer cell line that differentiates upon reaching confluency. This allows permeability studies on a cell model, which is reasonably similar to the human intestine.

Basically, the protocol is classical, the only peculiarity consisting in including ferrocyanide in post-fixation. I describe how I prepare and embed the membrane in order to obtain transverse sections of a cell monolayer because I find this is the only way to obtain regular sections with the cells sticking to the membrane (otherwise the ultrathin section splits between the cell and membrane).
Cold Temperature Preparation of XTEM Specimens of Embedded Metallic Nanoparticles
Authors: Johannessen Bernt , Llewellyn David J , Kluth Patrick , Ridgway Mark C
Published: March 2018

Nanoparticles (1-10 nm in diameter) are particularly susceptible to disorder, amorphization, deformation and/or dissolution upon ion irradiation as compared to their bulk counterparts, which is a consequence of the enhanced surface area to volume ratio of the former (structural disorder is often observed to be preferentially located at the surface). Synchrotron-radiation-based analytical techniques are ideally suited for the elucidation of structural perturbations as compared to the bulk material. Such techniques are commonly complemented by cross-sectional transmission electron microscopy (XTEM). XTEM offers invaluable information with respect to shape and morphology of the nanoparticles.

For the present work, Cu nanoparticles were synthesized within a 2 μm amorphous SiO2 matrix on a 520 μm Si support by ion implantation and thermal annealing following a procedure described elsewhere. In order to study the influence that ion irradiation has on the nanoparticles, the sample was then irradiated with 1x1015 ions / cm2 high-energy (5 MeV) Sn+ ions.
A ‘Different’ Kind of Microscopy
Authors: Schamber Fred , van Beek Kai
Published: March 2018

At the August M&M-2006 meeting in Chicago, we were standing next to our poster titled A Different Kind of Microscopy: Analyzing Features with an Automated Electron Beam when an acquaintance with long experience in electron microscopy wandered by. After a glance at the poster title, he challenged: “What's different about that?” Upon hearing our summary he asked (with what we took to be an encouraging tone of voice): “Are you going to publish this?” We had enough similar reactions from others to make that seem a good idea, and this is the result.

This discussion should begin by noting that the operative word in the title is “different,” not “new.” In point of fact, the foundations for the technique were laid in the 1970s when some workers began putting scanning electron microscopes and microprobes under software control by interfacing them to the “minicomputers” that powered the computerized x-ray analyzer units then entering the market. Even prior to this, there were a few “hard-wired” image analyzers that mechanized the process of extracting information from microscope images. Thus, automated analysis of features via an electron beam instrument is hardly a new concept.
Recent Developments in CrossBeam® Technology
Authors: Thesen A , Hoffmeister H , Schumann M , Gnauck P
Published: March 2018

Recent developments in nano- and semiconductor technology have substantially increased the demand for accurate and efficient site specific cross-sectioning of specimens and preparation of TEM samples. Moreover, nano-research is facing new challenges for manipulation, observation, and modification of devices on a submicron scale. At the same time in materials science a new focus on analytical nanoscale investigations—not only of specimen surfaces and cross sections—but on sample volumes is emerging.

These demanding requirements can be met if a focused ion beam (FIB) column for nanoscale structuring is combined with a high resolution SEM that is used to monitor the FIB milling and deposition process on a nanometer scale. Such an integrated Cross-Beam® system enables the high resolution observation and direct control of the FIB milling process in real time. Using this concept it is possible to prepare site specific TEM samples and cross sections with nano-scale accuracy. Such a system can be complemented with a gas injection system (GIS), for deposition and enhanced etching of specific materials, as well as, in-situ micro manipulation systems, and analytical detectors such as EDX and EBSP systems.
Part Ia: Case Study: Strategic plan for an EM Facility
Authors: Humphrey Elaine
Published: March 2018

I took over the facility in 1996. We had aging equipment, no assistance, there were huge budget cuts that year and I was told, “There was no money. The only money you're gonna get are your wages. Everything else has to come from user fees.” I had to find funds for service contracts and we had to increase our user base.

I figured I would have to find an assistant because there is no way one can run a TEM, an SEM and confocal and light microscope facilities alone. So I found a grant called “First Job in Science and Technology” which would give me a graduate student for one year, and we had a summer student who had just graduated and was looking for a job before she went on to graduate school. She learned really fast and by February she was excellent, but by May/June we were back into the same boat again.
Part Ib: How to Make a Business Plan for Facility Maintenance and Growth
Authors: Blewett Donald A
Published: March 2018

In case you didn't realize it, one of the things that is important about a business plan is to have an enthusiastic champion. I don't know if I've seen a person that has represented what she does more enthusiastically than Elaine did just now.

One of the reasons why I asked Elaine to go first was there's a lot of preparatory work that goes in place before you put together a business plan. Elaine did a very nice job in planning, and one of the key things in her Strategic Plan was that she took planning and made it a part of the business plan. A “S.W.O.T.” Analysis is an exercise that you go through when you are dealing with an enterprise that talks about Strengths, Weaknesses, Opportunities and Threats. Elaine put together the S.W.O.T. Analysis in addition to the current facility description and wish lists and that was extremely helpful in putting together her business plan.
Cross-sectional TEM Sample Preparation for Nanowires or Porous Films Grown on a Substrate
Authors: Song Chengyu
Published: March 2018

Nanowires or porous films grown on a substrate normally lack mechanical strength, and may be subject to damage during specimen preparation. When we made cross-sectional TEM specimen for this type of sample, we modified the traditional method by covering the sample with epoxy to improve the film strength, and applying single-section ion milling to protect the film from over-milling.

The sample surface is first covered with G1 epoxy. We choose G1 for this application because it is relatively thick and cures at low temperature. For samples with a dense-growth of nanowires or a thick porous film, a brief moment in vacuum helps to get rid of the air bubbles in the epoxy. The glue is cured at 100 degree C for 10 minutes, until its color turns to a reddish brown. To remove the excess glue and flatten the surface, the sample is then ground and polished until the glue is less than 0.1 mm thick.
Do Pathologists Use The Electron Microscope Enough?
Authors: W. Carmichael Stephen
Published: March 2018

The compound light microscope has been used by patholo gists for centuries, and remains the common tool for making a diagnosis. A half century ago, the electron microscope (EM) was introduced, and has aiso been proven to be a valuable, but expensive, tool. In the meantime, other tools and methods have worked their way into the pathologists’ armamentarium, with immunohistochemical, genetic, and molecular techniques being the most obvious examples. Josep Lloreta-Truil, Lola Ferrer, Teresa Ribalta, Marco Pavesi, and Sergio Serrano examined the literature to determine the frequency and appropriateness with which pathologists use the EM in their studies.
Nanomechanical Probing With Scanning Force Microscopy
Authors: Tsukruk V V , Gorbunov V V
Published: March 2018

Highly localized probing of surface nanomechanical properties with a submicron resolution can be accomplished with scanning probe microscopy (SPM). The SPM ability to probe local surface topography in conjunction with mechanical, adhesive, friction, thermal, magnetic, and electric properties is unique.1 However, the quantitative probing of the nanomechanical materials properties is still a challenge and only a few examples have been published to date.

In this note, we briefly review the latest developments in the nanomechanical probing of compliant materials (predominantly polymers). We solely focus our analysis of SPM-based approach in a so-called static force spectroscopy (SFS) mode.
Why Is My House So Dirty?
Authors: Benko James J
Published: March 2018

Today's newer homes are built to be energy efficient. Better insulation, better caulking, better windows restrict heat and airflow movements. Dust and contamination getting into the house has a harder time getting out. PLM examination of dust is a direct approach to assessing the magnitude of the problem and identifying the contamination responsible. Several actual cases of dust problems in the home and the role of microscopy in solving these problems are discussed.
Recycling Osmium Tetroxide
Authors: Kiernan John A
Published: March 2018

Osmium tetroxide is indeed wonderful stuff. Osmium is a rare element, so disposal of used solutions should consist of recycling, not dumping, even though osmium compounds are not considered environmentally hazardous (Smith et al., 1978 Trace Metal in the Environment, vol 4. Ann Arbor Science Publishers). The colorless and soluble toxic tetroxide. is rapidly reduced by almost any kind of dirt to a black, insoluble dioxide, usually in a colloidal form that's readily dispersed by moving water if it isn't firmly stuck to the solid organic matter that brought about the reduction.
Rotary Shadowing Macromolecules
Authors: Keene Douglas R
Published: March 2018

I'm somewhat amazed by how many varied techniques there are for rotary shadowing, and how few seem to agree with what works for us. So, here is our method.

We shadow biological molecules from the connective tissue matrix, usually ranging in size from 16 to 300 kilodaltons. Many are linear but some are globular. We spray the molecules in solution with 70% glycerol. The other 30% is 100 microgram/mL of protein, preferably in a volatile buffer such as 1% acetic acid or 0.1M ammonium bicarbonate, pH 7.8. Other buffers can be used, but salt crystals can be a big problem.
Turning Blood Cells into Oyster Shells
Authors: Carmichael Stephen W
Published: March 2018

The general consensus has been that the shells of mollusks form outside of cells. Akin to bone formation in vertebrates, an organic matrix is secreted by cells and the inorganic material is deposited within this matrix in an organized way. Andrew Mount, A.P. (Hap) Wheeler, Rajesh Paradkar, and Dennis Snider have now found convincing evidence that blood cells (specifically a class of granulocytic hemocytes) may be directly involved in shell crystal production for oysters.
Effects of Abbe Condenser Spherical Aberration on Image Quality
Authors: Clarke Theodore M
Published: March 2018

An earlier article in Microscopy Today, "Rediscovery of Darkfield Dispersion Staining while Building a Universal Student Microscope," noted that the darkfield inserts were made for Peter Cooke (MICA, Chicago, IL) to be used to teach high resolution dispersion staining in his advanced microscopy classes using Olympus BH2 microscopes and the Olympus 1.25 NA Abbe condenser. Peter has asked whether there is a better condenser design that will reduce the time and effort needed to switch between brightfield and darkfield.
Experience with a Dicing Saw for Rapid Pre-FIB TEM Sample Preparation
Authors: Conner Jim , James Beck  , Bryan Tracy
Published: March 2018

Since the publication of the use of a dicing saw for TEM sample preparation, several analytical labs have adopted this method as standard practice for site-specific cross section and plan view samples. In this article, we would like to provide additional practical details of these procedures, and describe several extensions, including useful notes on batch processing, preparing samples with an area of interest very close to the sample edge, and a Focused Ion Beam (FIB)-compatible sample holder. We present an unusual amount of detail in these processes to show some of the evolution of the method since its introduction and to allow others to easily reproduce these results.
Visualizing Gene Expression in Real-Time
Authors: Carmichael Stephen W
Published: March 2018

Gene expression has been visualized for a few decades, but in static forms such as blots and gene chips. Susan Janicki, Toshiro Tsukamoto, Sim one Salghetti, William Tansey, Ravi Sachidanandam, Kannanganattu Prasanth, Thomas Ried, Yaron Shav-Tal, Edouard Bertrand, Robert Singer, and David Spector have recently designed a cell line in which gene expression can be observed with stunningly accurate spatial and temporal resolution. Gene expression is a cascade of events beginning with transcription of RNA from the DNA template and ending with translation into a protein sequence. Janicki et al. were able to visualize the entire process at the levels of DNA, RNA, and proteins in living cells!
Ultra High Resolution SEM on Insulators and Contaminating Samples
Authors: Rice Trisha , Knowles Ralph
Published: March 2018

Historically, SEM developed as a high vacuum technique requiring sample chamber vacuum of 10-5 Torr or better. Energetic electrons scatter from any molecules they encounter, so their creation and transport from source to sample, through the focusing lenses of the electron column, requires high vacuum. This imposes a number of limitations on the kinds of samples that can be examined. Samples must tolerate the vacuum environment and the vacuum system must tolerate the sample. Generally, samples have to be solid, clean, dry, and not contain volatile components. Furthermore, since the vacuum insulates the sample from everything except the stub that supports it, non-conductive samples require a conductive pathway between the scanned region and ground to prevent the accumulation of charge deposited by the beam electrons.
Influence of Illumination Conditions on Temperature in Sample Cell and the Output of a Quadrant Detector in an Optical Tweezers System
Authors: Jiang Yuqiang , Guo Honglian , Liu Chunxiang , Li Zhaolin , Cheng Bingying , Zhang Daozhong , Jia Suotang
Published: March 2018

In an optical tweezers system, the output signal of a photodiode quadrant detector and the temperature in a sample cell are two key factors for the quantitative measurements of mechanical properties of living biological objects such as cells, organelles and macro-molecules. In order to enhance the output of a quadrant detector and effectively control the temperature in a sample cell, the dependence of the temperature in the sample cell and the output of the quadrant detector for different illumination conditions are studied. The results show that appropriate illumination conditions can ensure both nearly constant temperatures in the cell and the desired output signal, which provides for the possibility of highprecision and damage-free analysis of living biological objects.
Raman Microscopy as an Aid in Failure Analysis — Examples From the Lab
Authors: John Wolfgong W
Published: March 2018

Raman spectroscopy, much like the more familiar infrared spectroscopy, reveals chemical information of materials under investigation as a result of molecular vibrations. The result of these techniques, the spectrum, is a chemical "fingerprint" allowing for material identification. While infrared microscopy is well known and well established in the industrial laboratory setting, Raman microscopy has only recently begun a resurgence as a result of technological advances. These include advances in lasers, optical filters (notch filters), and CCD detector technologies.