Good Sample Quality Research Articles

Role of Flow Cytometry in the Diagnosis of Inborn Errors of Immunity

AbstractInborn errors of immunity (IEI) are a group of inherited heterogeneous disorders affecting the immune system characterized by increased susceptibility to infections, immune dysregulation, and lymphoproliferation. Flow cytometry (FCM) is a rapid and reliable technique for evaluation and enumeration of immune cells. It also helps in understanding the functional and signaling pathways of the immune system. Lymphocyte subset analysis is a simple and effective screening tool in suspected combined and humoral immunodeficiency patients. Qualitative phagocytic defects such as chronic granulomatous disease and leucocyte adhesion defect are easily diagnosed by FCM. Study of intracellular proteins (e.g., BTK, WASP, DOCK8), cytokine production, and signaling molecules (e.g., STAT3) by FCM is very useful but also quite challenging to establish. T and B lymphocyte interaction for normal class switching of B cells can be assessed and can help in diagnosis of combined variable immunodeficiency and hyperimmunoglobulin M syndrome. FCM is also used in posttransplant monitoring of IEI patients and also in prenatal diagnosis in suspected cases. It is also useful in validation of variants of uncertain significance obtained in exome sequencing. FCM results should always be interpreted with clinical history and, if needed, should be confirmed with molecular genetic studies before establishing the final diagnosis. Ensuring good sample quality and running parallel controls with patient samples will avoid the preanalytical and analytical errors. This review describes the applications of FCM in the diagnosis of various IEI.

Studying thermal transport in suspended monolayer molybdenum disulfide prepared by a nano-manipulator-assisted transfer method

The thermal transport of monolayer MoS2, grown by chemical vapor deposition (CVD) method, was studied in this work. A novel approach was developed to transfer monolayer MoS2 onto suspended microelectrothermal system device, where a nano-manipulator in a scanning electron microscope was employed to accomplish the feat. This nano-manipulator-assisted transferring gives a high sample yield with relatively good sample quality compared to the traditional wet/dry transfer methods. Temperature-dependent thermal conductivity of monolayer MoS2 was measured by suspended-pads thermal bridge technique, with thermal conductivity value slightly lower than the exfoliated samples due to the phonon-defects scattering for CVD grown samples. Further extension of the current transfer method was demonstrated on few-layer graphite, where suspended graphite flakes that were free of surface ripples and with high thermal conductance were shown.

Growth and Characterization of High In-content InGaN grown by MBE using Metal Modulated Epitaxy Technique (MME)

We investigated the growth and characterization of InGaN films with high In content up to 51.9% obtained by MBE MME-growth. Comparing the structural and optical properties of InGaN films grown using common growth method and MME technique, we could acquire the good quality of InGaN sample by MME-growth method with lower dislocation density, better composition uniformity and smoother surface. These experimental results suggest that MME has an enormous potential to promote the quality of high In-content InGaN materials and the development of InGaN-based devices. Besides, further study shows the process of MME growth, the parameters of material growth have opposite effects on the background carrier concentration and carrier mobility.

Validity of a rapid and simple fluorometric tripeptidyl peptidase 1 (TPP1) assay using dried blood specimens to diagnose CLN2 disease

PurposeCLN2 disease is a genetic disorder caused by dysfunction of the lysosomal enzyme tripeptidyl peptidase 1 (TPP1) that belongs to the neuronal ceroid lipofuscinoses (NCL) and leads to epilepsy, dementia, and death in young persons. CLN2 disease has recently become treatable by enzyme replacement, which can only be effective when the disease is diagnosed early. We have investigated the reliability of a test for TPP1 deficiency in dried blood specimens (DBS) to detect CLN2 disease. ResultsDuring a 12-year period we have received 3882 samples for testing TPP1. Quality of samples was checked by measuring two additional lysosomal enzyme activities. For 50 samples with subnormal TPP1 activity and good sample quality, we obtained adequate clinical and molecular genetic data. All 50 patients had doubtless evidence of CLN2 disease (including seven atypical patients) as shown by clinical findings and the presence of known pathogenic CLN2 variants. Our institution is a major reference center for NCL, and we have never received information that a patient with a normal DBS test was later diagnosed with CLN2 disease. ConclusionsWe consider our TPP1 test on DBS to be a reliable, convenient and inexpensive tool for a first diagnostic step in suspected CLN2 disease.

Feasibility of shotgun metagenomics to assess microbial ecology of pediatric tracheostomy tubes.

Biofilm formation on medical devices such as tracheostomy tubes (TTs) is a serious problem. The clinical impact of biofilms on the airway is still unclear. Biofilms may play a role in granulation tissue development, recurrent airway infections, and failure of laryngotracheal reconstructions. The microbial ecology on TTs has yet to be elucidated. The purpose of this study was to determine the feasibility of shotgun metagenomics to assess the biodistribution of microorganisms on TTs. Four TTs were collected from pediatric patients (1.4-10.2 years) with (n = 2) and without (n = 2) granulation tissue formation. Duration of TT placement prior to retrieval from patients ranged from 5 to 365 days. DNA extraction was performed using the MO BIO UltraClean Microbial Isolation (Mo Bio Laboratories, Carlsbad, CA). Library generation using Nextera XT adapters (Illumina Inc., San Diego, CA) and metagenomic shotgun sequencing was performed using the Illumina NextSeq500 (Illumina Inc, San Diego, CA). Salinibacter ruber, a species not found in mammalian microbiome communities, was used as a DNA standard and represented 0.7% to 5.7% of the microbiome, ensuring good quality and abundance of sample DNA. Metagenomic shotgun sequencing was successful for all patients. In TTs associated with granuloma, Fusobacterium nucleatum, Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae were predominant, most of which are considered pathogens. From TTs without granulomas, Neisseria mucosa, Neisseria sicca, Acinetobacter baumannii, and Haemophilus parainfluenzae were identified, primarily consistent with respiratory microbiome. This study reveals that metagenomic shotgun sequencing of biofilms formed on pediatric TTs is feasible with an apparent difference in microbiome for patients with granulation tissue. Further studies are necessary to elucidate the pathogenesis of microbial ecology and its role in airway disease in patients with TTs. 2c Laryngoscope, 129:317-323, 2019.

Fast Generation of Poisson-Disk Samples on Mesh Surfaces by Progressive Sample Projection

Generating well-distributed Poisson-disk samples with a blue noise power spectrum on 3D meshes is required by a wide range of applications in computer graphics. We introduce a novel method called Progressive Sample Projection that can generate massive Poisson-disk samples on mesh surfaces in very short time by projecting blue noise sample patterns from 2D planar space onto meshes. This parallel scheme can exploit full parallelism of GPU without deep recursion or atomic operations, which are often required by other methods. Compared with state-of-the-art methods, the effective generation rate of our method can be 2x to orders of magnitude faster, while still preserving good sample quality. This method is also progressive with memory usage bounded, thus being flexible for both performance and quality demanding work. The implementation is straightforward and easy to understand. It can be easily applied to adaptive sampling as well.

MnSi nanostructures obtained from epitaxially grown thin films: magnetotransport and Hall effect

We present a comparative study of the (magneto)transport properties, including Hall effect, of bulk, epitaxially grown thin film and nanostructured MnSi. In order to set our results in relation to published data we extensively characterize our materials, this way establishing a comparatively good sample quality. Our analysis reveals that in particular for thin film and nanostructured material, there are extrinsic and intrinsic contributions to the electronic transport properties, which by modeling the data we separate out. Finally, we discuss our Hall effect data of nanostructured MnSi under consideration of the extrinsic contributions and with respect to the question of the detection of a topological Hall effect in a skyrmionic lattice.

A Novel Cell Fixation Method that Greatly Enhances Protein Identification in Microproteomic Studies Using Laser Capture Microdissection and Mass Spectrometry.

Microproteomic studies have improved our knowledge of cell biology. Yet, with mass spectrometry (MS) analysis, accuracy can be lost for protein identification and quantification when using heterogeneous samples. Laser capture microdissection (LCM) allows for the enrichment of specific subsets of cells to study their proteome; however, sample fixation is necessary. Unfortunately, fixation hampers MS results due to protein cross-linking. The aim of this study was to identify both a fixation protocol and an extraction method that returns the best yield of proteins for downstream MS analysis, while preserving cellular structures. We compared glutaraldehyde (GLU), a common fixative to preserve cells, to dithiobispropionimidate (DTBP), a cleavable cross-linker. Our DTBP fixation/extraction protocol greatly increased the protein recovery. In fact, while 1000 GLU fixed cells returned only 159 unique protein hits, from 1464 unique peptides of 1994 unique collected spectra, 1000 DTBP fixed cells resulted in 567 unique collected protein hits, from 7542 unique peptides, of 10,401 unique collected spectra. That is, a 3.57-fold increase in protein hits, 5.15-fold increase in unique peptides, and a 5.22-fold increase in unique collected spectra. Overall, the novel protocol introduced here allows for a very efficient protein recovery and good sample quality for MS after sample collection using LCM.

Effect of Ti and Zn Doping on the Structural, Electric, and Magnetic Properties of GaFeO3

Multidoped (Zn,Ti) gallium orthoferrite [GaFeO3 and Ga0.98Zn0.02Fe0.98Ti0.02O3] ceramic was synthesized through a solid-state reaction. X-ray analysis of the prepared material provides its basic crystal data of a single-phase orthorhombic system. The scattered crystallite size and lattice strain of the material were estimated. Analysis of the micrograph of field emission scanning electron microscope shows uniform grain distribution in the sample, suggesting the formation of good quality of sample. Founded on the magnetic measurements, it is concluded that (Zn,Ti)-modified gallium ferrite has provided a reduction in the Curie temperature (TC); however, no significant changes in the magnetization values with Zn and Ti integration in GaFeO3 lattice. A noteworthy effect of substitution of multiple elements at the Ga and Fe sites on dielectric constant and tangent loss of GaFeO3 has been observed. Complete studies of temperature (180–400 K) and frequency (10–107 Hz) dependence of dielectric constant and impedance have provided the effect of grains and grain boundaries on the conduction mechanism and dielectric relaxation of the material.

Iron single crystal growth from a lithium-rich melt

α-Fe single crystals of rhombic dodecahedral habit were grown from a Li84N12Fe∼3 melt. Crystals of several millimeter along a side form at temperatures around T≈800°C. Upon further cooling the growth competes with the formation of Fe-doped Li3N. The b.c.c. structure and good sample quality of α-Fe single crystals were confirmed by X-ray and electron diffraction as well as magnetization measurements and chemical analysis. A nitrogen concentration of 90 ppm was detected by means of carrier gas hot extraction. Scanning electron microscopy did not reveal any sign of iron nitride precipitates.

Hydrothermal Synthesis and Multicolor Upconversion Fluorescence of Novel LiLuF4:Yb3+,Tm3+ Microcrystals.

LiLuF4:Yb3+,Tm3+ upconversion luminescence materials were synthesized by a hydrothermal method, in which NaF and NaBF4 were used as fluorine sources (labeled as sample A and B, respectively). Their morphologies, XRD patterns and UC emission properties were compared. The synthesized crystallites consist of regular octahedrons of several micrometers and aggregates. The XRD patterns indicate that they belong to tetragonal crystal system with 141/a space group. These microcrystals emit strong UC violet, visible and near infrared light under the excitation of 980 nm laser diode. The multicolor UC emissions from sample B are much stronger than those from sample A. The strong emission intensity is ascribed to good crystal quality of sample B.

Highly Transparent Wafer-Scale Synthesis of Crystalline WS2 Nanoparticle Thin Film for Photodetector and Humidity-Sensing Applications.

In the present investigation, we report a one-step synthesis method of wafer-scale highly crystalline tungsten disulfide (WS2) nanoparticle thin film by using a modified hot wire chemical vapor deposition (HW-CVD) technique. The average size of WS2 nanoparticle is found to be 25-40 nm over an entire 4 in. wafer of quartz substrate. The low-angle XRD data of WS2 nanoparticle shows the highly crystalline nature of sample along with orientation (002) direction. Furthermore, Raman spectroscopy shows two prominent phonon vibration modes of E(1)2g and A1g at ∼356 and ∼420 cm(-1), respectively, indicating high purity of material. The TEM analysis shows good crystalline quality of sample. The synthesized WS2 nanoparticle thin film based device shows good response to humidity and good photosensitivity along with good long-term stability of the device. It was found that the resistance of the films decreases with increasing relative humidity (RH). The maximum humidity sensitivity of 469% along with response time of ∼12 s and recovery time of ∼13 s were observed for the WS2 thin film humidity sensor device. In the case of photodetection, the response time of ∼51 s and recovery time of ∼88 s were observed with sensitivity ∼137% under white light illumination. Our results open up several avenues to grow other transition metal dichalcogenide nanoparticle thin film for large-area nanoelectronics as well as industrial applications.

Products analysis and new solution for multiple sample endoscope

Endoscopes are tubular devices used during laparoscopic procedures to examine the interior of the patient’s body for diagnosis purposes. During the procedure, small tools called biopsy micro forceps can be inserted through the endoscope to collect several living tissue samples for pathologic analysis. Even if the market proposes a large variety of micro forceps, it is not able to accomplish all the medical doctor requirements. For this reason, this article aims to identify and compare the characteristics of the products available on the market so to identify their lacks and improvement areas and to propose a new device able to respond to the physicians’ requests. In particular, the most critical aspects of the actual devices were identified by analysing patents and products and organising meetings with gastroenterologists and pathologists. According to the obtained results, a new concept of endoscope is presented. In particular, its design allows to reduce the surgery time, to increase the number and the quality of collected tissue samples and, at the same time, to guarantee good sample quality and to reduce the overall cost of the device and the procedure.

A universal fixation method based on quaternary ammonium salts (RNAlater) for omics-technologies: Saccharomyces cerevisiae as a case study

Genomics, transcriptomics, proteomics and fluxomics are powerful omics-technologies that play a major role in today's research. For each of these techniques good sample quality is crucial. Major factors contributing to the quality of a sample is the actual sampling procedure itself and the way the sample is stored directly after sampling. It has already been described that RNAlater can be used to store tissues and cells in a way that the RNA quality and quantity are preserved. In this paper, we demonstrate that quaternary ammonium salts (RNAlater) are also suitable to preserve and store samples from Saccharomyces cerevisiae for later use with the four major omics-technologies. Moreover, it is shown that RNAlater also preserves the cell morphology and the potential to recover growth, permitting microscopic analysis and yeast cell culturing at a later stage.

Single Crystal Growth and Characterization of the Iron-Based Superconductor KFe2As2Synthesized by KAs Flux Method

Centimeter sized platelet single crystals of KFe2As2 were grown using a self-flux method. An encapsulation technique using commercial stainless steel container allowed the stable crystal growth lasting for more than 2 weeks. Ternary K-Fe-As systems with various starting compositions were examined to determine the optimal growth conditions. Employment of KAs flux led to the growth of large single crystals with the typical size of as large as 15 mm x 10 mm x 0.4 mm. The grown crystals exhibit sharp superconducting transition at 3.4 K with the transition width 0.2 K, as well as the very large residual resistivity ratio exceeding 450, evidencing the good sample quality.

CITOLOGIA DE IMPRESSÃO DA SUPERFÍCIE OCULAR DE CÃES INFECTADOS NATURALMENTE POR <i>Leishmania (L.) chagasi</i>

Os cães domésticos são considerados o reservatório principal da Leishmania infantum (= Leishmania L.chagasi), o agente causal da Leishmaniose Visceral Canina (LVC). Sendo assim, a LVC tem umaimportância particular não somente para os clínicos veterinários, mas também à saúde pública. Entre sinaissistêmicos, incluem-se as alterações oculares com blefarite, conjuntivite, ceratoconjuntivite e ceratouveite. Oobjetivo deste trabalho foi avaliar os distúrbios da superfície ocular de cães com LVC com ou sem sinaisoculares por meio de citologia de impressão. Este método tem caráter não-invasivo, induz mínimo trauma eboa qualidade das amostras. Os animais foram divididos em três grupos: G1, constituído por 15 animaispositivos e apresentando sinais oculares de uveíte; G2, constituído por 15 animais positivos e sem sinaisoculares de uveíte e G3, constituído por 5 animais sadios. O material ocular foi coletado e processado,sendo subseqüentemente analisado obtendo-se informações de cada grupo. Os animais com sinaisoculares e sistêmicos apresentaram elevado infiltrado de polimorfonucleares e grande quantidade de debriscelulares e muco em comparação aos animais do grupo sem sinais oculares e grupo controle. Conclui-seque a citologia de impressão de cães com sinais oculares pode ser útil no diagnóstico presuntivo da doença,no entanto, os exames, parasitológico e sorológico, são essenciais no diagnóstico da LVC.

Properties of sol-gel derived YAG:Eu3+ hierarchical nanostructures with their time evolution studies

Eu 3 + doped yttrium aluminum garnet (YAG) nanoparticles were synthesized by sol-gel method. The samples were characterized by x-ray diffraction (XRD), transmission electron microscopy (TEM), and photoluminescence (PL) spectroscopy including vacuum ultraviolet (VUV) PL spectroscopy. XRD confirmed that each and every phases of YAG were present, indicating very good quality of sample. The crystallite size, estimated by XRD, increased from 10 to 30 nm with annealing temperatures and significant changes in morphology with annealing temperature was also found in TEM study. The particles were in spherical shape initially but agglomeration of particles started at higher temperatures resulting in hierarchical nanostructures having dimension more than 50 nm. The annealed YAG:Eu3+ hierarchical nanostructures showed strong red luminescence under VUV excitation, corresponding to D50→F72 transition. PL spectra also showed significant increase in luminescence intensity with the increase in annealing temperature. Time evolution studies were also performed continuously for 150 days to check the stability of prepared hierarchical nanostructures and were found to be extremely stable, making them one of the most feasible candidate for red phosphor and seize great potential in flat panel display application that underlies the importance of the current work.

Performing a percutaneous liver biopsy in parenchymal liver diseases

There are many ways of obtaining a liver biopsy sample but the percutaneous method is deemed as one of the simplest and safest methods. Percutaneous liver biopsy (PLB) is a commonly performed procedure carried out for the diagnosis and management of patients with parenchymal liver diseases. It plays a central role in providing histological assessment for either diagnostic or therapeutic purposes. This article describes how PLB is performed at the Royal Free Hospital radiology department, London, under ultrasound guidance, along with indications, contraindications, complications and advantages/disadvantages this method offers. Nursing implications are discussed in terms of assisting, caring and managing for these patients safely. This article aims to raise awareness of PLB and inform the reader how this tissue sample is taken, thus enabling further understanding of this procedure. It is concluded that the percutaneous route of obtaining a liver biopsy enables a good size and quality of sample to be taken in a safe and effective manner, with usually one pass being required with minimal associated complications.

3D-2D-3D photonic crystal heterostructures fabricated by direct laser writing

Using direct laser writing, we fabricate photoresist templates for 3D-2D-3D photonic crystal heterostructures for what we believe to be the first time. The optical properties of these structures are directly compared with the theoretical ideal, revealing good agreement and hence good sample quality. This provides an experimental starting point for the microfabrication and testing of broadband, 3D air-waveguide microcircuitry in photonic bandgap materials.

Characterizations of ZnTe bulks grown by temperature gradient solution growth

In this work, zinc telluride (ZnTe) bulk crystals have been grown for the first time by the temperature gradient solution growth (TGSG) technique. Hall effect and capacitance–voltage ( C– V) measurements were used to determine the room temperature electrical properties, and low temperature photoluminescence (PL) measurements were used to analyze the optical properties. As grown undoped ZnTe shows p-type conductivity with the carrier concentration (1–2) × 10 15 cm −3, mobility about 50 cm 2/V s, resistivity about 80–90 Ω cm. Otherwise, heavily doped p-ZnTe can be achieved by phosphorus doping. The carrier concentration demonstrates a logarithmic increase with the doping amount. The Hall carrier concentration up to 8×10 17 cm −3 (4.7×10 18 cm −3 from C– V measurement), resistivity low to around 0.15 Ω cm was achieved with a doping amount of 4000 ppm ZnP 2. Besides, the room temperature PL spectra exhibits a pure green luminescence of energy 2.259 eV ( λ=549.5 nm). The peak intensifies with increasing ZnP 2 doping amount and begins to saturate when the added amount is over 8000 ppm. The 9 K PL spectra also demonstrates that the excitonic zone is much more intense than for deep level band, indicating a good sample quality. It is plausible that using the TGSG technique can afford high-quality phosphorus-doped p-type ZnTe substrates for device applications.