Volumetric macromolecule identification in cryo-electron tomograms using capsule networks.

BACKGROUND: Despite recent advances in cellular cryo-electron tomography (CET), developing automated tools for macromolecule identification in submolecular resolution remains challenging due to the lack of annotated data and high structural complexities. To date, the extent of the deep learning methods constructed for this problem is limited to conventional Convolutional Neural Networks (CNNs). Identifying macromolecules of different types and sizes is a tedious and time-consuming task. In this paper, we employ a capsule-based architecture to automate the task of macromolecule identification, that we refer to as 3D-UCaps. In particular, the architecture is composed of three components: feature extractor, capsule encoder, and CNN decoder. The feature extractor converts voxel intensities of input sub-tomograms to activities of local features. The encoder is a 3D Capsule Network (CapsNet) that takes local features to generate a low-dimensional representation of the input. Then, a 3D CNN decoder reconstructs the sub-tomograms from the given representation by upsampling. RESULTS: We performed binary and multi-class localization and identification tasks on synthetic and experimental data. We observed that the 3D-UNet and the 3D-UCaps had an [Formula: see text]score mostly above 60% and 70%, respectively, on the test data. In both network architectures, we observed degradation of at least 40% in the [Formula: see text]-score when identifying very small particles (PDB entry 3GL1) compared to a large particle (PDB entry 4D8Q). In the multi-class identification task of experimental data, 3D-UCaps had an [Formula: see text]-score of 91% on the test data in contrast to 64% of the 3D-UNet. The better [Formula: see text]-score of 3D-UCaps compared to 3D-UNet is obtained by a higher precision score. We speculate this to be due to the capsule network employed in the encoder. To study the effect of the CapsNet-based encoder architecture further, we performed an ablation study and perceived that the [Formula: see text]-score is boosted as network depth is increased which is in contrast to the previously reported results for the 3D-UNet. To present a reproducible work, source code, trained models, data as well as visualization results are made publicly available. CONCLUSION: Quantitative and qualitative results show that 3D-UCaps successfully perform various downstream tasks including identification and localization of macromolecules and can at least compete with CNN architectures for this task. Given that the capsule layers extract both the existence probability and the orientation of the molecules, this architecture has the potential to lead to representations of the data that are better interpretable than those of 3D-UNet.

X-ray diffraction with micrometre spatial resolution for highly absorbing samples.

X-ray diffraction with high spatial resolution is commonly used to characterize (poly)crystalline samples with, for example, respect to local strain, residual stress, grain boundaries and texture. However, the investigation of highly absorbing samples or the simultaneous assessment of high-Z materials by X-ray fluorescence have been limited due to the utilization of low photon energies. Here, a goniometer-based setup implemented at the P06 beamline of PETRA III that allows for micrometre spatial resolution with a photon energy of 35 keV and above is reported. A highly focused beam was achieved by using compound refractive lenses, and high-precision sample manipulation was enabled by a goniometer that allows up to 5D scans (three rotations and two translations). As experimental examples, the determination of local strain variations in martensitic steel samples with micrometre spatial resolution, as well as the simultaneous elemental distribution for high-Z materials in a thin-film solar cell, are demonstrated. The proposed approach allows users from the materials-science community to determine micro-structural properties even in highly absorbing samples.

The role of occlusal loading in the pathogenesis of non-carious cervical lesions.

PURPOSE: To evaluate the putative role of occlusal loading in the pathogenesis of non-carious cervical lesions (NCCLs) in subjects who exhibited mixed excursive guidance [i.e., immediate canine guidance on one side and group function (GF) on the other]. METHODS: 20 subjects with Angle Class 1 occlusion and having from 1 to 5 NCCLs on separate teeth were selected. Only subjects who displayed mixed excursive guidance were recruited so that they could serve as their own controls. Non-carious cervical lesions were recorded on casts mounted in semi-adjustable articulators. RESULTS: On the GF sides, 22.5% of all teeth that contacted in working excursions exhibited NCCLs; only 2.1% of the teeth on the canine guided sides exhibited NCCLs, which were found exclusively in canines. Although a case for the multifactorial etiology of NCCLs remains strong, our data, albeit limited, seems to support the dominant role of occlusion in lesion formation.

The occlusal guard: a simplified technique for fabrication and equilibration.

Hard occlusal guards have been used effectively to treat myofacial pain originating from parafunctional activities. Also, they can protect the natural dentition when it opposes porcelain restorations, help to evaluate changes in occlusal vertical dimension during full mouth rehabilitation, minimize further tooth loss in patients with abfraction lesions, and redirect occlusal loads more favorably onto dental implant-supported prostheses. A simplified technique is described to fabricate a properly designed wax model of an occlusal guard that can be processed in acrylic in the same manner used to construct a complete denture.

Single tooth replacement utilizing implants in the esthetic zone: a case report.

Replacing a single tooth with an implant has become a common dental procedure; however, careful evaluation is necessary before placing one in the esthetic zone. Thorough diagnosis and planning - including the use of transposed diagnostic casts and cone beam computed tomography scans - can help dentists predict the final esthetic result prior to treatment, and help inform the patient of the potential result prior to performing any irreversible therapy. In the present case, the primary concern was the presurgical location of the facial free gingival margin (FGM) of the implant-supported crown, in relation to the adjacent teeth. Steps taken to correct the position of the facial FGM prior to implant placement led to a successful esthetic result.

Short-term objective and subjective evaluation of small-diameter implants used to support and retain mandibular prosthesis.

BACKGROUND: The introduction of small-diameter implants has provided dentists the means of providing edentulous and partially edentulous patients with immediate functioning transitional prostheses while definitive restorations are being fabricated. The successful use of these small-diameter implants for temporary stabilization of prostheses has led many clinicians to explore the option of using them as a definitive alternative, especially as the technique requires minimal time and also is economical for the patients. To date, there has been no study with multiple patients looking at both the subjective and objective outcomes of these small-diameter implants. MATERIALS AND METHODS: Twenty-seven edentulous patients were enrolled in this study, seven of them were smokers. One-hundred and eight small-diameter (2.0 mm, MDL) implants were surgically placed in 24 edentulous mandibles. All implants were immediately loaded. The patients filled out a screening questionnaire and four subsequent questionnaires to test their satisfaction with the altered prosthesis at 6, 12, 18 and 24 months. The survival of the implants was also noted. RESULTS: Smokers had an implant survival of 79%. Non-smokers had an implant survival of 100%. The results of the questionnaire indicated an overall satisfaction with the implant-supported prosthesis.

Developing a fixture level cast for implants with interfering axial convergence.

This article presents a novel technique for developing a master cast for two implants which are clinically placed convergent and very close to each other. The technique consists of making an implant level impression using a transfer coping for the posterior implant. Then fabricate a positional index intraorally, which contains a registration of the second transfer coping, the healing abutment reattached from the transfer in the impression and the adjacent teeth. The master cast is altered, using this positional index to incorporate the second implant analog.

A pooled analysis of six large-pen feedlot studies: effects of a noncoated initial and terminal implant compared with a single initial and delayed-release implant on arrival in feedlot heifers.

Randomized complete block design experiments (n = 6 experiments) evaluating steroidal implants (all from Merck Animal Health, Madison, NJ) were conducted in large-pen feedlot research facilities between 2015 and 2018 comparing an 80 mg trenbolone acetate (TBA) and 8 mg estradiol-17ß (E2) initial implant (Revalor-IH) and reimplanted with 200 mg TBA and 20 mg E2 (Revalor-200; REPEATED) to a single 80 mg TBA and 8 mg E2 uncoated; 120 mg TBA and 12 mg E2 coated implant (Revalor-XH) at arrival (SINGLE) on growth and carcass responses in finishing heifers. Experiments occurred in Nebraska, Oklahoma, Washington, and Texas. Similar arrival processing was used across experiments where 17,675 heifers [initial body weight = 333 kg SEM (4.1)] were enrolled into 180 pens (90 pens per treatment with 65-240 heifers per pen) and fed for 145-222 d. Only REPEATED heifers were removed from their pen at reimplant. Diets contained monensin and tylosin, consisted of ingredients common to each region, and contained greater than 90% concentrate. Ractopamine hydrochloride was fed for a minimum of 28 d prior to harvest. Linear mixed models were used for all analyses; model-adjusted means for each implant group and the corresponding SEM were generated. Distributions of U.S. Department of Agriculture (USDA) quality grade (QG) and yield grade (YG) were analyzed as ordinal outcomes. No differences (P ≥ 0.11) were detected for any performance parameters except dry matter intake (DMI), where SINGLE had greater (P = 0.02) DMI (9.48 vs. 9.38 ± 0.127 kg) compared with REPEATED. Heifers implanted with REPEATED had greater (P ≤ 0.02) hot carcass weight (HCW; 384 vs. 382 ± 2.8 kg), dressing percentage (64.54 vs. 64.22 ± 0.120%), and ribeye area (91.87 vs. 89.55 ± 0.839 cm2) but less (P ≤ 0.01) rib fat (1.78 vs. 1.83 ± 0.025 cm) and calculated YG (2.82 vs. 2.97 ± 0.040) and similar (P = 0.74) marbling scores (503 vs. 505 ± 5.2) compared with SINGLE heifers. Distributions of USDA YG and QG were impacted (P ≤ 0.03) by treatment such that REPEATED had fewer USDA Prime and YG 4 and 5 carcasses. Heifer growth performance did not differ between implant regimens, but HCW and muscling did, perhaps indicating that REPEATED may be suited for grid-based marketing, and SINGLE might be suited for heifers sold on a live basis depending upon market conditions and value-based grid premiums and discounts. However, these decisions are operational dependent and also may be influenced by factors including animal and employee safety, stress on animals, processing facilities, time of year, labor availability, and marketing strategies.

Immediate placement of implants and appliance in an irradiated patient: a case study.

PURPOSE: The purpose of this study was to evaluate the immediate placement of implants and appliance using hyperbaric oxygenation on a 45-year-old male with a history of squamous cell carcinoma of the floor of the mouth. MATERIALS: Five Nobel Biocare implants between the mental foamina were used along with a course of pre- and postsurgical hyperbaric oxygenation. RESULTS: After 39 months, the patient is symptom free and shows no signs of rejection. Conclusion Using an accepted hyperbaric oxygenation protocol when placing and restoring immediate implants in this patient resulted in a successful treatment outcome.

Building bridges between cellular and molecular structural biology.

The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.

Three-dimensional average-shape atlas of the honeybee brain and its applications.

The anatomical substrates of neural nets are usually composed from reconstructions of neurons that were stained in different preparations. Realistic models of the structural relationships between neurons require a common framework. Here we present 3-D reconstructions of single projection neurons (PN) connecting the antennal lobe (AL) with the mushroom body (MB) and lateral horn, groups of intrinsic mushroom body neurons (type 5 Kenyon cells), and a single mushroom body extrinsic neuron (PE1), aiming to compose components of the olfactory pathway in the honeybee. To do so, we constructed a digital standard atlas of the bee brain. The standard atlas was created as an average-shape atlas of 22 neuropils, calculated from 20 individual immunostained whole-mount bee brains. After correction for global size and positioning differences by repeatedly applying an intensity-based nonrigid registration algorithm, a sequence of average label images was created. The results were qualitatively evaluated by generating average gray-value images corresponding to the average label images and judging the level of detail within the labeled regions. We found that the first affine registration step in the sequence results in a blurred image because of considerable local shape differences. However, already the first nonrigid iteration in the sequence corrected for most of the shape differences among individuals, resulting in images rich in internal detail. A second iteration improved on that somewhat and was selected as the standard. Registering neurons from different preparations into the standard atlas reveals 1) that the m-ACT neuron occupies the entire glomerulus (cortex and core) and overlaps with a local interneuron in the cortical layer; 2) that, in the MB calyces and the lateral horn of the protocerebral lobe, the axon terminals of two identified m-ACT neurons arborize in separate but close areas of the neuropil; and 3) that MB-intrinsic clawed Kenyon cells (type 5), with somata outside the calycal cups, project to the peduncle and lobe output system of the MB and contact (proximate) the dendritic tree of the PE1 neuron at the base of the vertical lobe. Thus the standard atlas and the procedures applied for registration serve the function of creating realistic neuroanatomical models of parts of a neural net. The Honeybee Standard Brain is accessible at www.neurobiologie.fu-berlin.de/beebrain.

Unwarping confocal microscopy images of bee brains by nonrigid registration to a magnetic resonance microscopy image.

Confocal microscopy (CM) is a powerful image acquisition technique that is well established in many biological applications. It provides 3-D acquisition with high spatial resolution and can acquire several different channels of complementary image information. Due to the specimen extraction and preparation process, however, the shapes of imaged objects may differ considerably from their in vivo appearance. Magnetic resonance microscopy (MRM) is an evolving variant of magnetic resonance imaging, which achieves microscopic resolutions using a high magnetic field and strong magnetic gradients. Compared to CM imaging, MRM allows for in situ imaging and is virtually free of geometrical distortions. We propose to combine the advantages of both methods by unwarping CM images using a MRM reference image. Our method incorporates a sequence of image processing operators applied to the MRM image, followed by a two-stage intensity-based registration to compute a nonrigid coordinate transformation between the CM images and the MRM image. We present results obtained using CM images from the brains of 20 honey bees and a MRM image of an in situ bee brain.

Digital atlases of the antennal lobe in two species of tobacco budworm moths, the Oriental Helicoverpa assulta (male) and the American Heliothis virescens (male and female).

The antennal lobe of the moth brain is the primary olfactory center processing information about pheromones and plant odors. We present here a digital atlas of the glomerular antennal lobe structures in the male of Helicoverpa assulta and the male and female of Heliothis virescens, based on synaptic antibody staining combined with confocal microscopy. The numbers of the glomeruli in the three specimens were similar, 65, 66, and 62, respectively. Whereas the male antennal lobe has a macroglomerular complex consisting of three and four units in the two species, the female lobe has two enlarged glomeruli at a corresponding position, near the entrance of the antennal nerve. Another large glomerulus, showing homology in the three specimens, is ventrally located. The small size of the heliothine moths is advantageous for confocal microscopy because the entire brain can be visualized as a single image stack. The maps are freely accessible on the internet, and the digital form of the data allows each atlas to be rotated and sectioned at any angle, providing for the identification of glomeruli in different preparations.

Epithelial barrier modulation by a channel forming peptide.

NC-1059 is a synthetic channel-forming peptide that provides for ion transport across, and transiently reduces the barrier integrity of, cultured epithelial monolayers derived from canine kidney (MDCK cells). Experiments were conducted to determine whether epithelial cells derived from other sources were similarly affected. Epithelial cells derived from human intestine (T-84), airway (Calu-3), porcine intestine (IPEC-J2) and reproductive duct (PVD9902) were grown on permeable supports. Basal short circuit current (Isc) was <3 microA cm(-2) for T-84, IPEC-J2 and PVD9902 cell monolayers and <8 microA cm(-2) for Calu-3 cells. Apical NC-1059 exposure caused, in all cell types, an increase in Isc to >15 microA cm(-2), indicative of net anion secretion or cation absorption, which was followed by an increase in transepithelial conductance (in mS cm(-2): T-84, 1.6 to 62; PVD9902, 0.2 to 51; IPEC-J2, 0.3 to 26; Calu-3, 2.3 to 13). These results are consistent with the peptide affecting transcellular ion movement, with a likely effect also on the paracellular route. NC-1059 exposure increased dextran permeation when compared to basal permeation, which documents an effect on the paracellular pathway. In order to evaluate membrane ion channels, experiments were conducted to study the dose dependence and stability of the NC-1059-induced membrane conductance in Xenopus laevis oocytes. NC-1059 induced a dose-dependent increase in oocyte membrane conductance that remained stable for greater than 2 h. The results demonstrate that NC-1059 increases transcellular conductance and paracellular permeation in a wide range of epithelia. These effects might be exploited to promote drug delivery across barrier epithelia.

Honey bees navigate according to a map-like spatial memory.

By using harmonic radar, we report the complete flight paths of displaced bees. Test bees forage at a feeder or are recruited by a waggle dance indicating the feeder. The flights are recorded after the bees are captured when leaving the hive or the feeder and are released at an unexpected release site. A sequence of behavioral routines become apparent: (i) initial straight flights in which they fly the course that they were on when captured (foraging bees) or that they learned during dance communication (recruited bees); (ii) slow search flights with frequent changes of direction in which they attempt to "get their bearings"; and (iii) straight and rapid flights directed either to the hive or first to the feeding station and then to the hive. These straight homing flights start at locations all around the hive and at distances far out of the visual catchment area around the hive or the feeding station. Two essential criteria of a map-like spatial memory are met by these results: bees can set course at any arbitrary location in their familiar area, and they can choose between at least two goals. This finding suggests a rich, map-like organization of spatial memory in navigating honey bees.

Evaluation of atlas selection strategies for atlas-based image segmentation with application to confocal microscopy images of bee brains.

This paper evaluates strategies for atlas selection in atlas-based segmentation of three-dimensional biomedical images. Segmentation by intensity-based nonrigid registration to atlas images is applied to confocal microscopy images acquired from the brains of 20 bees. This paper evaluates and compares four different approaches for atlas image selection: registration to an individual atlas image (IND), registration to an average-shape atlas image (AVG), registration to the most similar image from a database of individual atlas images (SIM), and registration to all images from a database of individual atlas images with subsequent multi-classifier decision fusion (MUL). The MUL strategy is a novel application of multi-classifier techniques, which are common in pattern recognition, to atlas-based segmentation. For each atlas selection strategy, the segmentation performance of the algorithm was quantified by the similarity index (SI) between the automatic segmentation result and a manually generated gold standard. The best segmentation accuracy was achieved using the MUL paradigm, which resulted in a mean similarity index value between manual and automatic segmentation of 0.86 (AVG, 0.84; SIM, 0.82; IND, 0.81). The superiority of the MUL strategy over the other three methods is statistically significant (two-sided paired t test, P < 0.001). Both the MUL and AVG strategies performed better than the best possible SIM and IND strategies with optimal a posteriori atlas selection (mean similarity index for optimal SIM, 0.83; for optimal IND, 0.81). Our findings show that atlas selection is an important issue in atlas-based segmentation and that, in particular, multi-classifier techniques can substantially increase the segmentation accuracy.

A clinical pilot study of the dimensional accuracy of double-arch and complete-arch impressions.

STATEMENT OF PROBLEM: It has been suggested that articulated casts fabricated with the double-arch impression technique may have superior occlusal accuracy than those fabricated with a single complete-arch impression. However, lack of tray rigidity may lead to flexure of the impression/tray complex, resulting in inaccurate dies in the bucco-lingual dimension. PURPOSE: This clinical pilot study compared the dimensions of dies fabricated with 3 types of double-arch impressions to dies fabricated with the conventional complete-arch, custom tray method. MATERIAL AND METHODS: Thirty-five addition silicone impressions were made of cast metal copings cemented onto natural teeth prepared as complete-crown abutments. Four combinations of tray types and impression material viscosity were used: (1) complete-arch, custom acrylic trays loaded with heavy-bodied material; (2) double-arch, disposable plastic trays loaded with heavy-bodied material; (3) double-arch, disposable plastic trays loaded with putty material; and (4) double-arch, reusable brass metal trays loaded with heavy-bodied material. Immediately prior to tray insertion, light-bodied impression material was syringed over all copings as a wash. The 4 copings were fabricated from cast gold and simulated metal-ceramic complete-crown thimbles with polished collars and had "projections" on the occlusal surfaces. The impressions were poured in type IV die-stone. Bucco-lingual and inter-abutment dimensions were measured. The differences between the stone dimensions and cast metal control dimensions were calculated and converted to percent dimensional change. The data were analyzed with 1-way analysis of variance, Student t tests, and Mann-Whitney tests (P<.05). RESULTS: The plastic double-arch tray loaded with heavy-viscosity addition silicone and a low-viscosity wash produced the least accurate combination inter- and intra-abutment dimensions. For this protocol, 1.17% mean dimensional change was recorded. This result was significantly different than that obtained for the other 3 impression methods tested. No significant differences were found between the complete-arch method and protocols in which putty was loaded in a plastic or metal tray. CONCLUSION: Within the limitations of this pilot study, the more rigid tray/impression material combinations more accurately replicated stone dies.

Channel-forming peptide modulates transepithelial electrical conductance and solute permeability.

NC-1059, a synthetic channel-forming peptide, transiently increases transepithelial electrical conductance (g(TE)) and ion transport (as indicated by short-circuit current) across Madin-Darby canine kidney (MDCK) cell monolayers in a time- and concentration-dependent manner when apically exposed. g(TE) increases from <2 to >40 mS/cm(2) over the low to middle micromolar range. Dextran polymer (9.5 but not 77 kDa) permeates the monolayer following apical NC-1059 exposure, suggesting that modulation of the paracellular pathway accounts for changes in g(TE). However, concomitant alterations in junctional protein localization (zonula occludens-1, occludin) and cellular morphology are not observed. Effects of NC-1059 on MDCK g(TE) occur in nominally Cl(-)- and Na(+)-free apical media, indicating that permeation by these ions is not required for effects on g(TE), although two-electrode voltage-clamp assays with Xenopus oocytes suggest that both Cl(-) and Na(+) permeate NC-1059 channels with a modest Cl(-) permselectivity (P(Cl):P(Na) = 1.3). MDCK monolayers can be exposed to multiple NC-1059 treatments over days to weeks without diminution of response, alteration in the time course, or loss of responsiveness to physiological and pharmacological secretagogues. Together, these results suggest that NC-1059 represents a valuable tool to investigate tight junction regulation and may be a lead compound for therapeutic interventions.