A neutral matter-wave microscope (NEMI): Design and setup

Matter wave microscopes such as electron microscopes or helium ion microscopes are vital tools in numerous fields of sciences. This thesis presents the design of a new matter wave microscope using neutral helium atoms as imaging probe. In contrast to the already well established helium atom scattering techniques where information about the surface is obtained through diffraction and spectroscopy analysis, Nemi (short for NEutral helium MIcroscopy) uses a focused beam of neutral ground-state helium atoms to image the surface of a sample. The main advantages which set this technique aside from already existing scanning probe techniques is that the helium probe has a much lower energy (less than 100 meV) for a de Broglie wavelength of less than 0.1 nm and that the helium atoms are uncharged and chemically inert. This means that the Nemi technique is in principle equally suitable for insulators, semiconductors, metals and organic samples provided they are vacuum compatible. The new Nemi technique is also particularly suited for the investigation of fragile samples. The focusing of the neutral helium beam is realized with a so called Fresnel zone plate. As a part of this thesis it is shown, for the first time, that sub-micron focusing with this type of diffraction grating is possible. A complete design concept for the microscope including a detailed evaluation of the expected helium flow rates in the probe beam as well as of the background gas between the vacuum chambers is presented. The functionality and technical design for the different components are discussed. First test results characterizing the probe beam of the assembled beam column are presented

Image formation in the scanning helium microscope

The scanning helium microscope (SHeM) is a new addition to the array of available microscopies, particularly for delicate materials that may suffer damage under techniques utilising light or charged particles. As with all other microscopies, the specifics of image formation within the instrument are required to gain a full understanding of the produced micrographs. We present work detailing the basics of the subject for the SHeM, including the specific nature of the projection distortions that arise due to the scattering geometry. Extension of these concepts allowed for an iterative ray tracing Monte Carlo model replicating diffuse scattering from a sample surface to be constructed. Comparisons between experimental data and simulations yielded a minimum resolvable step height of (67 ± 5) µm and a minimum resolvable planar angle of (4.3 ± 0.3)° for the instrument in question.acceptedVersio

Desenvolvimento de um método molecular para detecção e identificação de Xanthomonas campestris pv. viticola

ABSTRACTCom o objetivo de desenvolver um método molecular para detecção e identificação de Xanthomonas campestris pv. viticola (Xcv), agente causal do cancro bacteriano da videira, oligonucleotídeos (primers) foram desenhados com base na seqüência parcial do gene hrpB. As combinações de primers Xcv1F/Xcv3R e RST2/Xcv3R que amplificaram fragmentos de 243 e 340 pb, respectivamente, foram testadas quanto à especificidade e sensibilidade para detecção do DNA de Xcv. Com os dois pares de primers, amplificação foi positiva com o DNA de 44 isolados de Xcv, mas também com quatro isolados de X.c. pv. mangiferaeindicae e cinco de X. axonopodis pv. passiflorae. Contudo, a digestão dos produtos de PCR permitiu diferenciar Xcv dos isolados desses patovares. Nenhum dos dois pares de primers amplificou o DNA de videira, nem de 20 bactérias não patogênicas isoladas da flora da videira, ou de 10 isolados de outros seis gêneros de bactérias fitopatogênicas. A sensibilidade dos primers Xcv1F/Xcv3R e RST2/Xcv3R foi de 10 pg e 1 pg de DNA purificado de Xcv, respectivamente. O limite de detecção de RST2/Xcv3R foi de 104 UFC/ml, mas empregando-se uma segunda rodada de amplificação com o primer interno Xcv1F, esse limite foi de 102 UFC/ml. Não foi possível detectar por PCR a presença de Xcv usando-se, diretamente na reação, o extrato do macerado de pecíolos de videira previamente inoculados. Entretanto, amplificações foram positivas quando se utilizou uma etapa de enriquecimento em meio de cultura antes da PCR. Detectou-se Xcv em 1 µl da suspensão obtida do lavado das placas e em uma suspensão obtida a partir de uma única colônia. A identidade da bactéria foi confirmada pela análise de RFLP dos produtos de amplificação dos primers RST2/Xcv3R com HaeIII.In order to develop a molecular method for detection and identification of Xanthomonas campestris pv. viticola (Xcv) the causal agent of grapevine bacterial canker, primers were designed based on the partial sequence of the hrpB gene. Primer pairs Xcv1F/Xcv3R and RST2/Xcv3R, which amplified 243- and 340-bp fragments, respectively, were tested for specificity and sensitivity in detecting DNA from Xcv. Amplification was positive with DNA from 44 Xcv strains and with DNA from four strains of X. campestris pv. mangiferaeindicae and five strains of X. axonopodis pv. passiflorae, with both primer pairs. However, the enzymatic digestion of PCR products could differentiate Xcv strains from the others. None of the primer pairs amplified DNA from grapevine, from 20 strains of nonpathogenic bacteria from grape leaves and 10 strains from six representative genera of plant pathogenic bacteria. Sensitivity of primers Xcv1F/Xcv3R and RST2/Xcv3R was 10 pg and 1 pg of purified Xcv DNA, respectively. Detection limit of primers RST2/Xcv3R was 104 CFU/ml, but this limit could be lowered to 102 CFU/ml with a second round of amplification using the internal primer Xcv1F. Presence of Xcv in tissues of grapevine petioles previously inoculated with Xcv could not be detected by PCR using macerated extract added directly in the reaction. However, amplification was positive with the introduction of an agar plating step prior to PCR. Xcv could be detected in 1 µl of the plate wash and from a cell suspension obtained from a single colony. Bacterium identity was confirmed by RFLP analysis of the RST2/Xcv3R amplification products digested with Hae III

Variation of bending rigidity with material density: bilayer silica with nanoscale holes

Two dimensional (2D) materials are a young class of materials that is foreseen to play an important role as building blocks in a range of applications, e.g. flexible electronics. For such applications, mechanical properties such as the bending rigidity κ are important. Only a few published measurements of the bending rigidity are available for 2D materials. Nearly unexplored is the question of how the 2D material density influences the bending rigidity. Here, we present helium atom scattering measurements on a “holey” bilayer silica with a density of 1.4 mg m−2, corresponding to 1.7 monolayers coverage. We find a bending rigidity of 6.6 ± 0.3 meV, which is lower than previously published measurements for a complete 2D film, where a value of 8.8 ± 0.5 meV was obtained. The decrease of bending rigidity with lower density is in agreement with theoretical predictions.publishedVersio

Fast resolution change in neutral helium atom microscopy

In neutral helium atom microscopy, a beam of atoms is scanned across a surface. Though still in its infancy, neutral helium microscopy has seen a rapid development over the last few years. The inertness and low energy of the helium atoms (less than 0.1 eV) combined with a very large depth of field and the fact that the helium atoms do not penetrate any solid material at low energies open the possibility for a non-destructive instrument that can measure topology on the nanoscale even on fragile and insulating surfaces. The resolution is determined by the beam spot size on the sample. Fast resolution change is an attractive property of a microscope because it allows different aspects of a sample to be investigated and makes it easier to identify specific features. However up till now it has not been possible to change the resolution of a helium microscope without breaking the vacuum and changing parts of the atom source. Here we present a modified source design, which allows fast, step wise resolution change. The basic design idea is to insert a moveable holder with a series of collimating apertures in front of the source, thus changing the effective source size of the beam and thereby the spot size on the surface and thus the microscope resolution. We demonstrate a design with 3 resolution steps. The number of resolution steps can easily be extended.publishedVersio

Temperature-Dependent Bending Rigidity of AB-Stacked Bilayer Graphene

The change in bending rigidity with temperature κ(T) for 2D materials is highly debated: theoretical works predict both increase and decrease. Here we present measurements of κ(T), for a 2D material: AB-stacked bilayer graphene. We obtain κ(T) from phonon dispersion curves measured with helium atom scattering in the temperature range 320–400 K. We find that the bending rigidity increases with temperature. Assuming a linear dependence over the measured temperature region we obtain κ(T)=[(1.3 ± 0.1) + (0.006 ± 0.001)T/K] eV by fitting the data. We discuss this result in the context of existing predictions and room temperature measurements.publishedVersio

Human fallopian tube: a new source of multipotent adult mesenchymal stem cells discarded in surgical procedures

<p>Abstract</p> <p>Background</p> <p>The possibility of using stem cells for regenerative medicine has opened a new field of investigation. The search for sources to obtain multipotent stem cells from discarded tissues or through non-invasive procedures is of great interest. It has been shown that mesenchymal stem cells (MSCs) obtained from umbilical cords, dental pulp and adipose tissue, which are all biological discards, are able to differentiate into muscle, fat, bone and cartilage cell lineages. The aim of this study was to isolate, expand, characterize and assess the differentiation potential of MSCs from human fallopian tubes (hFTs).</p> <p>Methods</p> <p>Lineages of hFTs were expanded, had their karyotype analyzed, were characterized by flow cytometry and underwent <it>in vitro </it>adipogenic, chondrogenic, osteogenic, and myogenic differentiation.</p> <p>Results</p> <p>Here we show for the first time that hFTs, which are discarded after some gynecological procedures, are a rich additional source of MSCs, which we designated as <it>human tube MSCs </it>(htMSCs).</p> <p>Conclusion</p> <p>Human tube MSCs can be easily isolated, expanded <it>in vitro</it>, present a mesenchymal profile and are able to differentiate into muscle, fat, cartilage and bone <it>in vitro</it>.</p

Effect of Internet-Based Cognitive Behavioral Humanistic and Interpersonal Training vs Internet-Based General Health Education on Adolescent Depression in Primary Care A Randomized Clinical Trial

Importance Although 13% to 20% of American adolescents experience a depressive episode annually, no scalable primary care model for adolescent depression prevention is currently available. Objective To study whether competent adulthood transition with cognitive behavioral humanistic and interpersonal training (CATCH-IT) lowers the hazard for depression in at-risk adolescents identified in primary care, as compared with a general health education (HE) attention control. Design, Setting, and Participants This multicenter, randomized clinical trial, a phase 3 single-blind study, compares CATCH-IT with HE. Participants were enrolled from 2012 to 2016 and assessed at 2, 6, 12, 18, and 24 months postrandomization in a primary care setting. Eligible adolescents were aged 13 to 18 years with subsyndromal depression and/or history of depression and no current depression diagnosis or treatment. Of 2250 adolescents screened for eligibility, 446 participants completed the baseline interview, and 369 were randomized into CATCH-IT (n = 193) and HE (n = 176). Interventions The internet-based intervention, CATCH-IT, is a 20-module (15 adolescent modules and 5 parent modules) online psychoeducation course that includes a parent program, supported by 3 motivational interviews. Main Outcomes and Measures Time to event for depressive episode; depressive symptoms at 6 months. Results Of 369 participants (mean [SD] age, 15.4 [1.5] years; 251 women [68%]) included in this trial, 193 were randomized into CATCH-IT and 176 into HE. Among these participants, 28% had both a past episode and subsyndromal depression; 12% had a past episode only, 59% had subsyndromal depression only, and 1% had borderline subsyndromal depression. The outcome of time to event favored CATCH-IT but was not significant with intention-to-treat analyses (unadjusted hazard ratio [HR], 0.59; 95% CI, 0.27-1.29; P = .18; adjusted HR, 0.53; 95% CI, 0.23-1.23; P = .14). Adolescents with higher baseline Center for Epidemiologic Studies Depression scale (CES-D10) scores showed a significantly stronger effect of CATCH-IT on time to event relative to those with lower baseline scores (HR 0.82; 95% CI, 0.67-0.99; P = .04). For example, the hazard ratio for a CES-D10 score of 15 was 0.20 (95% CI, 0.05-0.77), compared with a hazard ratio of 1.44 (95% CI, 0.41-5.03) for a CES-D10 score of 5. In both CATCH-IT and HE groups, depression symptoms declined and functional scores increased. Conclusions and Relevance For preventing depressive episodes CATCH-IT may be better than HE for at-risk adolescents with subsyndromal depression. Also CATCH-IT may be a scalable approach to prevent depressive episodes in adolescents in primary care. Trial Registration ClinicalTrials.gov Identifier: NCT0189374

The Impact of Histopathological Features on the Prognosis of Oral Squamous Cell Carcinoma : A Comprehensive Review and Meta-Analysis

ObjectiveOver many decades, studies on histopathological features have not only presented high-level evidence of contribution for treatment directions and prognosis of oral squamous cell carcinoma (OSCC) but also provided inconsistencies, making clinical application difficult. The 8th TNM staging system of OSCC has acknowledged the importance of some histopathological features, by incorporating depth of invasion (DOI) to T category and extranodal extension (ENE) to N category. The aim of this systematic review with meta-analysis is to determine the most clinically relevant histopathological features for risk assessment and treatment planning of OSCC and to elucidate gaps in the literature. MethodsA systematic review was conducted using PRISMA guidelines, and the eligibility criteria were based on population, exposure, comparison, outcome, and study type (PECOS). PubMed, Cochrane, Scopus, and Web of Science were searched for articles exploring the impact of histopathological features on OSCC outcomes with Cox multivariate analysis. Pooled data were subjected to an inverse variance method with random effects or fixed effect model, and the risk of bias was evaluated using quality in prognosis studies (QUIPS). Quality of evidence was assessed with the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) criteria. ResultsThe study included 172 articles published from 1999 to 2021. Meta-analyses confirmed the prognostic potential of DOI, ENE, perineural invasion, lymphovascular invasion, and involvement of the surgical margins and brought promising results for the association of bone invasion, tumor thickness, and pattern of invasion with increased risk for poor survival. Although with a small number of studies, the results also revealed a clinical significance of tumor budding and tumor-stroma ratio on predicted survival of patients with OSCC. Most of the studies were considered with low or moderate risk of bias, and the certainty in evidence varied from very low to high. ConclusionOur results confirm the potential prognostic usefulness of many histopathological features and highlight the promising results of others; however, further studies are advised to apply consistent designs, filling in the literature gaps to the pertinence of histopathological markers for OSCC prognosis. Systematic Review RegistrationInternational Prospective Register of Systematic Reviews (PROSPERO), identifier CRD42020219630.Peer reviewe

Artificial neural networks on eggs production data management

Background: Eggs have acquired a greater importance as an inexpensive and high-quality protein. The Brazilian egg industry has been characterized by a constant production expansion in the last decade, increasing the number of housed animals and facilitating the spread of many diseases. In order to reduce the sanitary and financial risks, decisions regard¬ing the production and the health status of the flock must be made based on objective criteria. The use of Artificial Neural Networks (ANN) is a valuable tool to reduce the subjectivity of the analysis. In this context, the aim of this study was at validating the ANNs as viable tool to be employed in the prediction and management of commercial egg production flocks. Materials, Methods & Results: Data from 42 flocks of commercial layer hens from a poultry company were selected. The data refer to the period between 2010 and 2018 and it represents a total of 600,000 layers. Six parameters were selected as “output” data (number of dead birds per week, feed consumption, number of eggs, weekly weight, weekly egg produc¬tion and flock uniformity) and a total of 13 parameters were selected as “input” data (flock age, flock identification, total hens in the flock, weekly weight, flock uniformity, lineage, weekly mortality, absolute number of dead birds, eggs/hen, weekly egg production, feed consumption, flock location, creation phase). ANNs were elaborated by software programs NeuroShell Predictor and NeuroShell Classifier. The programs identified input variables for the assembly of the networks seeking the prediction of the variables called outgoing that are subsequently validated. This validation goes through the comparison between the predictions and the real data present in the database that was the basis for the work. Validation of each ANN is expressed by the specific statistical parameters multiple determination (R2) and Mean Squared Error (MSE). For instance, R2 above 0.70 expresses a good validation. ANN developed for the output variable “number of dead birds per week” presented R2= 0.9533 and MSE= 256.88. For “feed consumption”, the results were R2= 0.7382 and MSE= 274.56. For “number of eggs (eggs/hen)”, the results were R2= 0.9901 and MSE= 172.26. For “weekly weight”, R2= 0.9712 and MSE= 11154.41. For “weekly egg production”, R2= 0.8015 and MSE= 72.60. For “flock uniformity”, R2= -2.9955 and MSE= 431.82. Discussion: From the six ANN designed in this study, in five it was possible to validate the predictions by comparing predictions with the real data. In one output parameter (“flock uniformity”), it was not possible to have adequate validation due to insufficient data in our database. For “number of dead birds per week”, “feed consumption”, “weekly weight” and “uniformity”, the most important variable was “flock age” (27.5%, 52.5%, 55.2% and 37.9%, respectively). For “number of eggs (eggs/hen)”, “uniformity” (52.1%) was the most relevant variable for prediction. For “weekly egg production”, “flock age” and “number of eggs (eggs/hen)” were the most important zootechnical parameters, both with a relative contribution of 38.2%. The results showed that even with the use of a robust tool such as ANNs, it is necessary to have well-noted and clear information that expresses the reality of the flocks. In any case, the results presented allow us to state that ANNs are capable for the management of data generated in a commercial egg production facility. The process of evaluation of these data would be improved if ANNs were routinely used by the professionals linked to this activity