Secretory origin and temporal appearance of the porcine beta-microseminoprotein (sperm motility inhibitor) in the boar reproductive system

A specific antiserum against the porcine sperm motility inhibitor (SMI) was used in Western blotting analysis of tissue homogenates to reveal the possible origin of SMI in the boar reproductive system at different ages. The ages of the boar used were day 0, day 15, day 30, day 60, day 100, day 120, day 135, day 150, and day 210. The tissue homogenates of the day 60 and older showed immunoreaction. The results were further checked by indirect immunohistochemical staining and observed under light microscope. The SMI antigen appeared in the epithelial cells and in the lumen of the secretory ducts of the prostate gland. These results indicate that porcine SMI is synthesized only by the postnatal prostate gland. The homogenate of the prostate gland of day 100 was also used for the purification of SMI. The prostatic SMI was co-eluted with the seminal SMI in the reversed phase HPLC. Mass spectrometric analysis of the prostatic SMI revealed a molecular weight of 10,066. These results indicate that the prostatic SMI is identical to that purified from seminal plasma (Jeng et al., 1993; Biochem Biophys Res Communi 191:435-440).     

Visualization of macromolecular complexes using cryo-electron microscopy with FEI Tecnai transmission electron microscopes

This protocol details the steps used for visualizing the frozen-hydrated grids as prepared following the accompanying protocol entitled 'Preparation of macromolecular complexes for visualization using cryo-electron microscopy.' This protocol describes how to transfer the grid to the microscope using a standard cryo-transfer holder or, alternatively, using a cryo-cartridge loading system, and how to collect low-dose data using an FEI Tecnai transmission electron microscope. This protocol also summarizes and compares the various options that are available in data collection for three-dimensional (3D) single-particle reconstruction. These options include microscope settings, choice of detectors and data collection strategies both in situations where a 3D reference is available and in the absence of such a reference (random-conical and common lines).     

Direct stochastic optical reconstruction microscopy with standard fluorescent probes

Direct stochastic optical reconstruction microscopy (dSTORM) uses conventional fluorescent probes such as labeled antibodies or chemical tags for subdiffraction resolution fluorescence imaging with a lateral resolution of ～20 nm. In contrast to photoactivated localization microscopy (PALM) with photoactivatable fluorescent proteins, dSTORM experiments start with bright fluorescent samples in which the fluorophores have to be transferred to a stable and reversible OFF state. The OFF state has a lifetime in the range of 100 milliseconds to several seconds after irradiation with light intensities low enough to ensure minimal photodestruction. Either spontaneously or photoinduced on irradiation with a second laser wavelength, a sparse subset of fluorophores is reactivated and their positions are precisely determined. Repetitive activation, localization and deactivation allow a temporal separation of spatially unresolved structures in a reconstructed image. Here we present a step-by-step protocol for dSTORM imaging in fixed and living cells on a wide-field fluorescence microscope, with standard fluorescent probes focusing especially on the photoinduced fine adjustment of the ratio of fluorophores residing in the ON and OFF states. Furthermore, we discuss labeling strategies, acquisition parameters, and temporal and spatial resolution. The ultimate step of data acquisition and data processing can be performed in seconds to minutes.     

Imaging three-dimensional tissue architectures by focused ion beam scanning electron microscopy

In this protocol, we describe a 3D imaging technique known as 'volume electron microscopy' or 'focused ion beam scanning electron microscopy (FIB/SEM)' applied to biological tissues. A scanning electron microscope equipped with a focused gallium ion beam, used to sequentially mill away the sample surface, and a backscattered electron (BSE) detector, used to image the milled surfaces, generates a large series of images that can be combined into a 3D rendered image of stained and embedded biological tissue. Structural information over volumes of tens of thousands of cubic micrometers is possible, revealing complex microanatomy with subcellular resolution. Methods are presented for tissue processing, for the enhancement of contrast with osmium tetroxide/potassium ferricyanide, for BSE imaging, for the preparation and platinum deposition over a selected site in the embedded tissue block, and for sequential data collection with ion beam milling; all this takes approximately 90 h. The imaging conditions, procedures for alternate milling and data acquisition and techniques for processing and partitioning the 3D data set are also described; these processes take approxiamtely 30 h. The protocol is illustrated by application to developing chick cornea, in which cells organize collagen fibril bundles into complex, multilamellar structures essential for transparency in the mature connective tissue matrix. The techniques described could have wide application in a range of fields, including pathology, developmental biology, microstructural anatomy and regenerative medicine.     

Focus: Addiction: Smoking Use and Cessation Among People with Serious Mental Illness

Smoking rates in people with serious mental illness (SMI) are disproportionately high compared to the general population. It is a leading contributor to the early mortality in this population. Smoking cessation rates are low in this group, though patients are motivated to quit. Unfortunately, health care providers do not always prioritize smoking cessation for this population. This review provides an overview of prevalence rates, biological effects that maintain smoking, and evidence-based treatments for smoking cessation in SMI. In addition, objective and qualitative data from a chart review of 78 patients with SMI prescribed smoking cessation treatment at one community mental health center are described. Of these, 30 (38.5 percent) were found to either quit (16/78) or reduce (14/78) smoking. Varenicline appeared to be particularly effective. Review of the literature and results of this study suggest that smoking cessation pharmacotherapies are effective for SMI patients and should be offered to those who smoke.     

Single-molecule pull-down for studying protein interactions

This protocol describes a single-molecule pull-down (SiMPull) assay for analyzing physiological protein complexes. The assay combines the conventional pull-down assay with single-molecule total internal reflection fluorescence (TIRF) microscopy and allows the probing of single macromolecular complexes directly from cell or tissue extracts. In this method, antibodies against the protein of interest are immobilized on a passivated microscope slide. When cell extracts are applied, the surface-tethered antibody captures the protein together with its physiological interaction partners. After washing away the unbound components, single-molecule fluorescence microscopy is used to probe the pulled-down proteins. Captured proteins are visualized through genetically encoded fluorescent protein tags or through antibody labeling. Compared with western blot analysis, this ultrasensitive assay requires considerably less time and reagents and provides quantitative data. Furthermore, SiMPull can distinguish between multiple association states of the same protein. SiMPull is generally applicable to proteins from a variety of cellular contexts and to endogenous proteins. Starting with the cell extracts and passivated slides, the assay requires 1.5-2.5 h for data acquisition and analysis.     

A protocol to analyse cellular dynamics during plant development

In vivo microscopy generates images that contain complex information on the dynamic behaviour of three-dimensional (3D) objects. As a result, adapted mathematical and computational tools are required to help in their interpretation. Ideally, a complete software chain to study the dynamics of a complex 3D object should include: (i) the acquisition, (ii) the preprocessing and (iii) segmentation of the images, followed by (iv) a reconstruction in time and space and (v) the final quantitative analysis. Here, we have developed such a protocol to study cell dynamics at the shoot apical meristem in Arabidopsis. The protocol uses serial optical sections made with the confocal microscope. It includes specially designed algorithms to automate the identification of cell lineage and to analyse the quantitative behaviour of the meristem surface.     

Validation of the sperm quality analyzer (SQA) for dog sperm analysis

In the present study, a simple and inexpensive unit (the Sperm Quality Analyzer-SQA), was evaluated for dog sperm analysis. Our objective was to propose a cheap, accurate and convenient device to be used in veterinary practices involved with dog fertility assessment and artificial insemination. The device was tested by analyzing repeatability and accuracy at different sperm concentrations and motility characteristics. The Sperm Motility Index (SMI), a numeric index provided by the SQA, was compared with the results obtained using a computer-aided sperm analyzer (Hamilton Thorn IVOS 10). The correlation between SMI and some sperm parameters as well as predictive values of the SMI were established. The dog sperm data provided by the SQA were consistent and repeatable (coefficient of variability below 10% for all concentrations tested). The SMI was significantly dependant on motile sperm concentration and a positive significant correlation was established for the different motile sperm concentrations from a concentration of 25 x 10(6) up to over 200 x 10(6) cells/mL. Zero motility did not affect SMI because non-motile cells, regardless of their concentration, do not cause any fluctuations in the optical density (OD). Over the tested 200 x 10(6) cells/mL value, a correlation still could be observed but it was not statistically significant, possibly because of a saturation of the system. In dog semen, the correlation is better between SMI values and the number of motile spermatozoa than with the overall motile concentration. Based on this observation, a predictive value was given to the SMI allowing for a sorting of dog ejaculates in 3 sperm categories (SMI <100, 100250) each characterized by a range of sperm number and motility. If a positive correlation between the SMI categories and fertility has been demonstrated in humans, such a correlation needs to be established in dogs.     

Clustering of physical health multimorbidity in people with severe mental illness: An accumulated prevalence analysis of United Kingdom primary care data

BackgroundPeople with severe mental illness (SMI) have higher rates of a range of physical health conditions, yet little is known regarding the clustering of physical health conditions in this population. We aimed to investigate the prevalence and clustering of chronic physical health conditions in people with SMI, compared to people without SMI.Methods and findingsWe performed a cohort-nested accumulated prevalence study, using primary care data from the Clinical Practice Research Datalink (CPRD), which holds details of 39 million patients in the United Kingdom. We identified 68,783 adults with a primary care diagnosis of SMI (schizophrenia, bipolar disorder, or other psychoses) from 2000 to 2018, matched up to 1:4 to 274,684 patients without an SMI diagnosis, on age, sex, primary care practice, and year of registration at the practice. Patients had a median of 28.85 (IQR: 19.10 to 41.37) years of primary care observations. Patients with SMI had higher prevalence of smoking (27.65% versus 46.08%), obesity (24.91% versus 38.09%), alcohol misuse (3.66% versus 13.47%), and drug misuse (2.08% versus 12.84%) than comparators. We defined 24 physical health conditions derived from the Elixhauser and Charlson comorbidity indices and used logistic regression to investigate individual conditions and multimorbidity. We controlled for age, sex, region, and ethnicity and then additionally for health risk factors: smoking status, alcohol misuse, drug misuse, and body mass index (BMI). We defined multimorbidity clusters using multiple correspondence analysis (MCA) and K-means cluster analysis and described them based on the observed/expected ratio. Patients with SMI had higher odds of 19 of 24 conditions and a higher prevalence of multimorbidity (odds ratio (OR): 1.84; 95% confidence interval [CI]: 1.80 to 1.88, p < 0.001) compared to those without SMI, particularly in younger age groups (males aged 30 to 39: OR: 2.49; 95% CI: 2.27 to 2.73; p < 0.001; females aged 18 to 30: OR: 2.69; 95% CI: 2.36 to 3.07; p < 0.001). Adjusting for health risk factors reduced the OR of all conditions. We identified 7 multimorbidity clusters in those with SMI and 7 in those without SMI. A total of 4 clusters were common to those with and without SMI; while 1, heart disease, appeared as one cluster in those with SMI and 3 distinct clusters in comparators; and 2 small clusters were unique to the SMI cohort. Limitations to this study include missing data, which may have led to residual confounding, and an inability to investigate the temporal associations between SMI and physical health conditions.ConclusionsIn this study, we observed that physical health conditions cluster similarly in people with and without SMI, although patients with SMI had higher burden of multimorbidity, particularly in younger age groups. While interventions aimed at the general population may also be appropriate for those with SMI, there is a need for interventions aimed at better management of younger-age multimorbidity, and preventative measures focusing on diseases of younger age, and reduction of health risk factors.

In an observational analysis of primary care data from the UK, Naomi Launders and colleagues study the prevalence and clustering of physical health conditions and multimorbidity in individuals with severe mental illnesses.     

Using Light Sheet Fluorescence Microscopy to Image Zebrafish Eye Development

Light sheet fluorescence microscopy (LSFM) is gaining more and more popularity as a method to image embryonic development. The main advantages of LSFM compared to confocal systems are its low phototoxicity, gentle mounting strategies, fast acquisition with high signal to noise ratio and the possibility of imaging samples from various angles (views) for long periods of time. Imaging from multiple views unleashes the full potential of LSFM, but at the same time it can create terabyte-sized datasets. Processing such datasets is the biggest challenge of using LSFM. In this protocol we outline some solutions to this problem. Until recently, LSFM was mostly performed in laboratories that had the expertise to build and operate their own light sheet microscopes. However, in the last three years several commercial implementations of LSFM became available, which are multipurpose and easy to use for any developmental biologist. This article is primarily directed to those researchers, who are not LSFM technology developers, but want to employ LSFM as a tool to answer specific developmental biology questions. Here, we use imaging of zebrafish eye development as an example to introduce the reader to LSFM technology and we demonstrate applications of LSFM across multiple spatial and temporal scales. This article describes a complete experimental protocol starting with the mounting of zebrafish embryos for LSFM. We then outline the options for imaging using the commercially available light sheet microscope. Importantly, we also explain a pipeline for subsequent registration and fusion of multiview datasets using an open source solution implemented as a Fiji plugin. While this protocol focuses on imaging the developing zebrafish eye and processing data from a particular imaging setup, most of the insights and troubleshooting suggestions presented here are of general use and the protocol can be adapted to a variety of light sheet microscopy experiments.     

Advantages of the scanning ion microscopy for mapping halogen corticoids in normal and transformed cells in culture

Summary— The intra-cellular distribution of eight halogen glucocorticoids was investigated by ion microscopy in two cellular varieties of cultured non-cancer cells (fibroblast 3T3) and cancer cells (human breast tumor cells MCF-7). Two types of ion microscopy helped to determine this distribution, a direct imaging ion microscope (SMI 300) with low spatial resolution, and a scanning ion microscope (IMS4F), featuring high resolution, serving to obtain maps representing the intra-cellular distribution of the fluorine elements and drugs present in these monolayer cultured cells. The fluorine images representative of the drugs containing fluorine showed that these drugs are essentially concentrated in the cell nuclei. In these nuclei, the distribution of these drugs is different from that of heterochromatin and of the nucleolus.     

In vivo imaging of subcutaneous structures using functional photoacoustic microscopy

Functional photoacoustic microscopy (fPAM) is a hybrid technology that permits noninvasive imaging of the optical absorption contrast in subcutaneous biological tissues. fPAM uses a focused ultrasonic transducer to detect high-frequency photoacoustic (PA) signals. Volumetric images of biological tissues can be formed by two-dimensional raster scanning, and functional parameters can be further extracted from spectral measurements. fPAM is safe and applicable to animals as well as humans. This protocol provides guidelines for parameter selection, system alignment, imaging operation, laser safety and data processing for in vivo fPAM. It currently takes approximately 100 min to carry out this protocol, including approximately 50 min for data acquisition using a 10-Hz pulse-repetition-rate laser system. The data acquisition time, however, can be significantly reduced by using a laser system with a higher pulse repetition rate.     

Association of environmental and socioeconomic indicators with serious mental illness diagnoses identified from general practitioner practice data in England: A spatial Bayesian modelling study

BackgroundThe evidence is sparse regarding the associations between serious mental illnesses (SMIs) prevalence and environmental factors in adulthood as well as the geographic distribution and variability of these associations. In this study, we evaluated the association between availability and proximity of green and blue space with SMI prevalence in England as a whole and in its major conurbations (Greater London, Birmingham, Liverpool and Manchester, Leeds, and Newcastle).Methods and findingsWe carried out a retrospective analysis of routinely collected adult population (≥18 years) data at General Practitioner Practice (GPP) level. We used data from the Quality and Outcomes Framework (QOF) on the prevalence of a diagnosis of SMI (schizophrenia, bipolar affective disorder and other psychoses, and other patients on lithium therapy) at the level of GPP over the financial year April 2014 to March 2018. The number of GPPs included ranged between 7,492 (April 2017 to March 2018) to 7,997 (April 2014 to March 2015) and the number of patients ranged from 56,413,719 (April 2014 to March 2015) to 58,270,354 (April 2017 to March 2018). Data at GPP level were converted to the geographic hierarchy unit Lower Layer Super Output Area (LSOA) level for analysis. LSOAs are a geographic unit for reporting small area statistics and have an average population of around 1,500 people. We employed a Bayesian spatial regression model to explore the association of SMI prevalence in England and its major conurbations (greater London, Birmingham, Liverpool and Manchester, Leeds, and Newcastle) with environmental characteristics (green and blue space, flood risk areas, and air and noise pollution) and socioeconomic characteristics (age, ethnicity, and index of multiple deprivation (IMD)). We incorporated spatial random effects in our modelling to account for variation at multiple scales.Across England, the environmental characteristics associated with higher SMI prevalence at LSOA level were distance to public green space with a lake (prevalence ratio [95% credible interval]): 1.002 [1.001 to 1.003]), annual mean concentration of PM_2.5 (1.014 [1.01 to 1.019]), and closeness to roads with noise levels above 75 dB (0.993 [0.992 to 0.995]). Higher SMI prevalence was also associated with a higher percentage of people above 24 years old (1.002 [1.002 to 1.003]), a higher percentage of ethnic minorities (1.002 [1.001 to 1.002]), and more deprived areas.Mean SMI prevalence at LSOA level in major conurbations mirrored the national associations with a few exceptions. In Birmingham, higher average SMI prevalence at LSOA level was positively associated with proximity to an urban green space with a lake (0.992 [0.99 to 0.998]). In Liverpool and Manchester, lower SMI prevalence was positively associated with road traffic noise ≥75 dB (1.012 [1.003 to 1.022]). In Birmingham, Liverpool, and Manchester, there was a positive association of SMI prevalence with distance to flood zone 3 (land within flood zone 3 has ≥1% chance of flooding annually from rivers or ≥0.5% chance of flooding annually from the sea, when flood defences are ignored): Birmingham: 1.012 [1.000 to 1.023]; Liverpool and Manchester: 1.016 [1.006 to 1.026]. In contrast, in Leeds, there was a negative association between SMI prevalence and distance to flood zone 3 (0.959 [0.944 to 0.975]). A limitation of this study was because we used a cross-sectional approach, we are unable to make causal inferences about our findings or investigate the temporal relationship between outcome and risk factors. Another limitation was that individuals who are exclusively treated under specialist mental health care and not seen in primary care at all were not included in this analysis.ConclusionsOur study provides further evidence on the significance of socioeconomic associations in patterns of SMI but emphasises the additional importance of considering environmental characteristics alongside socioeconomic variables in understanding these patterns. In this study, we did not observe a significant association between green space and SMI prevalence, but we did identify an apparent association between green spaces with a lake and SMI prevalence. Deprivation, higher concentrations of air pollution, and higher proportion of ethnic minorities were associated with higher SMI prevalence, supporting a social-ecological approach to public health prevention. It also provides evidence of the significance of spatial analysis in revealing the importance of place and context in influencing area-based patterns of SMI.

In a cross-sectional study, Joana Cruz and colleagues study the relationship between environmental and socioeconomic factors and prevalence of serious mental illness in England between 2014 and 2018.     

Progress report of the TUDAB project for automated cancer cell detection.

Two methods for high resolution cell image data acquisition are applied routinely. Cells are either scanned by a computer controlled fast scanning microscope photometer (SMP) or a TV-camera. The software system for digital image analysis was completely revised and implemented on the PR 330 minicomputer. The system contains codes for primary cell data acquisition, segmentation of cells, cell feature extraction and statistical cell analysis. With this system, SMP and TV scanned cell data bases of PAP stained cells in vaginal smears, grouped into several classes, have been built up. Each data base contains 34 primary features and 20 feature combinations for each cell. A linear discriminant analysis is applied routinely for cell classification. The present state of the system and its operation are described, cell features and classification results are shown, and future steps for a prescreening strategy are discussed.     

L’AQS (Analyseur de la Qualité du Sperme): Evaluation de son intérêt pour l’analyse,la sélection et la congélation des spermatozoïdes

The sperm quality analyzer (SQA) is a device which has been recently proposed to make an objective measurement of human semen quality. It is based on a simple physical method: the measurement of optical density modifications induced by sperm movement. Optical density modification are measured though an electro-optical photoreceptor. Analogical signals produced are transformed in numerical signals and analysed by a microprocessor. The result of the analysis is given in a unique value called «sperm motility index» (SMI). In this study the reproducibility of the results got with the SQA has been measured and the interests of this new diagnostic technique for the andrological laboratory and for human sperm freezing have been evaluated. It can be conclude that SMI measurement is simple, well reproductive and very useful to evaluate the overall quality of a sample. The SMI allows a good prediction of the efficiency of the methods used to select spermatozoa so it can help to choose the best technique, in order to prepare the spermatozoa for a medically assisted procreation. Values of SMI after freezing and thawing of semen samples were also reproducible. They were well correlated to the number of motil sperm per straw as measured by conventional methods, SMI was more objective and accurate. From the value of SMI measured on fresh samples it was possible to predict the freezing tolerance. Therefore measurement of SMI could be very useful to check straws quality and in studies on human semen cryopreservation. Prospective studies are further needed to determine if the SMI could also predict “in vivo” fertility of IVF results and fertilizing ability of frozen thawed sperm.     

Two-parameter data acquisition system for rapid slit-scan analysis of mammalian chromosomes

A data acquisition system is described for recording two independent signals simultaneously from a laser-based flow cytometer for rapid slit-scan chromosome analysis. High-aperture microscope optics allow recording of fluorescence distributions along the longest axis of metaphase chromosomes with a spatial resolution better than 1 micron. Fluorescence and small angle forward light scatter as well as dual-wavelength fluorescence signals from Indian muntjac chromosomes stained with propidium iodide (PI) or acridine orange (AO) have been recorded simultaneously. While maintaining the multi-user operation of the computer, photomultiplier signals are digitized at a rate of 400 signals per second, stored temporarily in high-speed cache memories, and transferred subsequently to a minicomputer for further storage. Extensive software packages for data acquisition, analysis, and display of the results are described. Data acquisition is generally done in list mode, allowing complete reconstruction of individual signals (profiles) at any time. The distribution of stained constituents along the chromosomes can be displayed. Furthermore, histograms of various parameters of the input signals may be generated.     

Atomic structure of a single large biomolecule from diffraction patterns of random orientations

The short and intense pulses of the new X-ray free electron lasers, now operational or under construction, may make possible diffraction experiments on single molecule-sized objects with high resolution, before radiation damage destroys the sample. In a single molecule imaging (SMI) experiment thousands of diffraction patterns of single molecules with random orientations are recorded. One of the most challenging problems of SMI is how to assemble these noisy patterns of unknown orientations into a consistent single set of diffraction data. Here we present a new method which can solve the orientation problem of SMI efficiently even for large biological molecules and in the presence of noise. We show on simulated diffraction patterns of a large protein molecule, how the orientations of the patterns can be found and the structure to atomic resolution can be solved. The concept of our algorithm could be also applied to experiments where images of an object are recorded in unknown orientations and/or positions like in cryoEM or tomography.     

Scaled body‐mass index shows how habitat quality influences the condition of four fish taxa in north‐eastern Spain and provides a novel indicator of ecosystem health

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In vitro Biofilm Formation in an 8-well Chamber Slide

The chronic nature of many diseases is attributed to the formation of bacterial biofilms which are recalcitrant to traditional antibiotic therapy. Biofilms are community-associated bacteria attached to a surface and encased in a matrix. The role of the extracellular matrix is multifaceted, including facilitating nutrient acquisition, and offers significant protection against environmental stresses (e.g. host immune responses). In an effort to acquire a better understanding as to how the bacteria within a biofilm respond to environmental stresses we have used a protocol wherein we visualize bacterial biofilms which have formed in an 8-well chamber slide. The biofilms were stained with the BacLight Live/Dead stain and examined using a confocal microscope to characterize the relative biofilm size, and structure under varying incubation conditions. Z-stack images were collected via confocal microscopy and analyzed by COMSTAT. This protocol can be used to help elucidate the mechanism and kinetics by which biofilms form, as well as identify components that are important to biofilm structure and stability.     

Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography

In cryo-electron tomography (cryo-ET) of biological samples, the quality of tomographic reconstructions can vary depending on the transmission electron microscope (TEM) instrument and data acquisition parameters. In this paper, we present Parakeet, a ‘digital twin’ software pipeline for the assessment of the impact of various TEM experiment parameters on the quality of three-dimensional tomographic reconstructions. The Parakeet digital twin is a digital model that can be used to optimize the performance and utilization of a physical instrument to enable in silico optimization of sample geometries, data acquisition schemes and instrument parameters. The digital twin performs virtual sample generation, TEM image simulation, and tilt series reconstruction and analysis within a convenient software framework. As well as being able to produce physically realistic simulated cryo-ET datasets to aid the development of tomographic reconstruction and subtomogram averaging programs, Parakeet aims to enable convenient assessment of the effects of different microscope parameters and data acquisition parameters on reconstruction quality. To illustrate the use of the software, we present the example of a quantitative analysis of missing wedge artefacts on simulated planar and cylindrical biological samples and discuss how data collection parameters can be modified for cylindrical samples where a full 180° tilt range might be measured.